def create_helix_hydrogen_bond_proxies(params,
pdb_hierarchy,
selection_cache,
weight,
hbond_counts,
distance_ideal,
distance_cut,
remove_outliers,
restrain_hbond_angles,
log=sys.stdout):
assert (not None in [distance_ideal, distance_cut])
generated_proxies = geometry_restraints.shared_bond_simple_proxy()
hb_angle_proxies = []
helix_class = params.helix_type
if helix_class == "alpha":
helix_step = 4
elif helix_class == "pi":
helix_step = 5
elif helix_class == "3_10":
helix_step = 3
else:
print >> log, " Don't know bonding for helix class %s." % helix_class
return generated_proxies, hb_angle_proxies
try:
helix_selection = selection_cache.selection(params.selection)
except Exception, e:
print >> log, str(e)
return generated_proxies, hb_angle_proxies
def create_helix_hydrogen_bond_proxies (
params,
pdb_hierarchy,
selection_cache,
weight,
hbond_counts,
distance_ideal,
distance_cut,
remove_outliers,
log=sys.stdout) :
assert (not None in [distance_ideal, distance_cut])
generated_proxies = geometry_restraints.shared_bond_simple_proxy()
helix_class = params.helix_type
if helix_class == "alpha" :
helix_step = 4
elif helix_class == "pi" :
helix_step = 5
elif helix_class == "3_10" :
helix_step = 3
else :
print >> log, " Don't know bonding for helix class %s." % helix_class
return generated_proxies
try :
helix_selection = selection_cache.selection(params.selection)
except Exception, e :
print >> log, str(e)
return generated_proxies
def __init__(self, *args, **kwds):
super(restrained_crystal_structure_builder,
self).__init__(*args, **kwds)
geom = geometry_restraints
adp = adp_restraints
self._proxies = {}
self._proxies = {
'bond':
geometry_restraints.shared_bond_simple_proxy(),
'angle':
geometry_restraints.shared_angle_proxy(),
'dihedral':
geometry_restraints.shared_dihedral_proxy(),
'planarity':
geometry_restraints.shared_planarity_proxy(),
'chirality':
geometry_restraints.shared_chirality_proxy(),
'bond_similarity':
geometry_restraints.shared_bond_similarity_proxy(),
'adp_similarity':
adp_restraints.shared_adp_similarity_proxy(),
'rigid_bond':
adp_restraints.shared_rigid_bond_proxy(),
'isotropic_adp':
adp_restraints.shared_isotropic_adp_proxy(),
'fixed_u_eq_adp':
adp_restraints.shared_fixed_u_eq_adp_proxy(),
'adp_u_eq_similarity':
adp_restraints.shared_adp_u_eq_similarity_proxy(),
'adp_volume_similarity':
adp_restraints.shared_adp_volume_similarity_proxy(),
}
def __init__(O,
sites_cart,
geometry_restraints_manager,
geometry_restraints_flags,
lbfgs_termination_params,
lbfgs_exception_handling_params):
O.grm = geometry_restraints_manager
cs = O.grm.crystal_symmetry
sst = O.grm.site_symmetry_table
sites_frac = cs.unit_cell().fractionalize(sites_cart)
O.x = sst.pack_coordinates(sites_frac=sites_frac)
O.proxies = geometry_restraints.shared_bond_simple_proxy()
for i_seq,pair_sym_dict in enumerate(O.grm.shell_sym_tables[0]):
for j_seq,sym_ops in pair_sym_dict.items():
assert i_seq <= j_seq
bond_params = O.grm.bond_params_table[i_seq][j_seq]
for rt_mx_ji in sym_ops:
O.proxies.append(geometry_restraints.bond_simple_proxy(
i_seqs=[i_seq, j_seq],
rt_mx_ji=rt_mx_ji,
params=bond_params))
def get_target_result():
f, _ = O.compute_functional_and_gradients()
return dev_target_result(
target=f,
n_bond_proxies=O.proxies.size(),
bond_residual_sum=f)
O.first_target_result = get_target_result()
import scitbx.lbfgs
O.minimizer = scitbx.lbfgs.run(
target_evaluator=O,
termination_params=lbfgs_termination_params,
exception_handling_params=lbfgs_exception_handling_params)
f, _ = O.compute_functional_and_gradients()
O.final_target_result = get_target_result()
def get_basepair_hbond_proxies(
pdb_hierarchy,
bp_phil_params,
hbond_distance_cutoff=3.4):
assert pdb_hierarchy is not None
bond_proxies_result = []
angle_proxies_result = []
if len(bp_phil_params) > 0:
# return bond_proxies_result, angle_proxies_result
selection_cache = pdb_hierarchy.atom_selection_cache()
pdb_atoms = pdb_hierarchy.atoms()
# dashes = open('dashes.pml', 'w')
pdb_atoms = pdb_hierarchy.atoms()
for base_pair in bp_phil_params:
if (base_pair.base1 is not None and base_pair.base2 is not None
and base_pair.enabled):
selected_atoms_1 = selection_cache.iselection(base_pair.base1)
selected_atoms_2 = selection_cache.iselection(base_pair.base2)
if len(selected_atoms_1) == 0:
raise Sorry("Selection %s in base_pair retusulted in 0 atoms." % (
base_pair.base1))
if len(selected_atoms_2) == 0:
raise Sorry("Selection %s in base_pair retusulted in 0 atoms." % (
base_pair.base2))
a1 = pdb_atoms[selected_atoms_1[0]]
a2 = pdb_atoms[selected_atoms_2[0]]
if base_pair.saenger_class == 0:
hbonds, saenger_class = get_h_bonds_for_basepair(
a1, a2, distance_cutoff=hbond_distance_cutoff,
log=sys.stdout, verbose=-1)
base_pair.saenger_class = saenger_class
hbonds = get_h_bonds_for_particular_basepair((a1, a2), base_pair.saenger_class)
for hb in hbonds:
dist = hb[0].distance(hb[1])
if dist < hbond_distance_cutoff:
if base_pair.restrain_hbonds:
hb_target, hb_sigma = get_hb_lenght_targets(hb)
p = geometry_restraints.bond_simple_proxy(
i_seqs=[hb[0].i_seq, hb[1].i_seq],
distance_ideal=hb_target,
weight=1.0/hb_sigma**2,
slack=0,
top_out=False,
limit=1,
origin_id=1)
bond_proxies_result.append(p)
# print "bond:", hb[0].id_str(), hb[1].id_str(), "(%4.2f, %4.2f)" % (hb_target, hb_sigma)
# s1 = pdb_atoms[hb[0].i_seq].id_str()
# s2 = pdb_atoms[hb[1].i_seq].id_str()
# ps = "dist chain \"%s\" and resi %s and name %s, chain \"%s\" and resi %s and name %s\n" % (
# s1[14:15], s1[15:19], s1[5:8], s2[14:15], s2[15:19], s2[5:8])
# dashes.write(ps)
if base_pair.restrain_hb_angles:
angle_proxies_result += get_angle_proxies_for_bond(hb)
else:
print "NA hbond rejected:",hb[0].id_str(), hb[1].id_str(), "distance=%.2f" % dist
# dashes.close()
return geometry_restraints.shared_bond_simple_proxy(bond_proxies_result), \
angle_proxies_result
class bond_restraint_test_case(geometry_restraints_test_case):
manager = restraints.manager(
bond_proxies=geometry_restraints.shared_bond_simple_proxy([
geom.bond_simple_proxy((0, 30), 1.42, 1),
geom.bond_simple_proxy((1, 21), 1.42, 1)
]))
proxies = manager.bond_proxies
restraint_t = geom.bond
def __init__(self, *args, **kwds):
super(restrained_crystal_structure_builder, self).__init__(*args, **kwds)
geom = geometry_restraints
adp = adp_restraints
self._proxies = {}
self._proxies = {
'bond': geometry_restraints.shared_bond_simple_proxy(),
'angle': geometry_restraints.shared_angle_proxy(),
'dihedral': geometry_restraints.shared_dihedral_proxy(),
'planarity': geometry_restraints.shared_planarity_proxy(),
'chirality': geometry_restraints.shared_chirality_proxy(),
'bond_similarity': geometry_restraints.shared_bond_similarity_proxy(),
'adp_similarity': adp_restraints.shared_adp_similarity_proxy(),
'rigid_bond': adp_restraints.shared_rigid_bond_proxy(),
'isotropic_adp': adp_restraints.shared_isotropic_adp_proxy(),
'fixed_u_eq_adp': adp_restraints.shared_fixed_u_eq_adp_proxy(),
'adp_u_eq_similarity': adp_restraints.shared_adp_u_eq_similarity_proxy(),
'adp_volume_similarity': adp_restraints.shared_adp_volume_similarity_proxy(),
}
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
def create_sheet_hydrogen_bond_proxies(sheet_params,
pdb_hierarchy,
selection_cache,
weight,
hbond_counts,
distance_ideal,
distance_cut,
remove_outliers,
restrain_hbond_angles,
log=sys.stdout):
assert (not None in [distance_ideal, distance_cut])
angle_restraint_type = 0
if restrain_hbond_angles:
angle_restraint_type = 3
prev_strand = sheet_params.first_strand
prev_selection = selection_cache.selection(prev_strand)
hb_angle_proxies = []
prev_rgs = _get_residue_groups_from_selection(
pdb_hierarchy=pdb_hierarchy, bool_selection=prev_selection)
n_proxies = 0
k = 0
generated_proxies = geometry_restraints.shared_bond_simple_proxy()
while k < len(sheet_params.strand):
curr_strand = sheet_params.strand[k]
curr_selection = selection_cache.selection(curr_strand.selection)
curr_start = None
prev_start = None
if curr_strand.bond_start_current is not None:
curr_start = selection_cache.selection(
curr_strand.bond_start_current)
if curr_strand.bond_start_previous is not None:
prev_start = selection_cache.selection(
curr_strand.bond_start_previous)
curr_rgs = _get_residue_groups_from_selection(
pdb_hierarchy=pdb_hierarchy, bool_selection=curr_selection)
i = j = 0
len_prev_residues = len(prev_rgs)
len_curr_residues = len(curr_rgs)
if curr_start is not None and prev_start is not None:
if curr_start.count(True) < 1 or prev_start.count(True) < 1:
error_msg = """\
Wrong registration in SHEET record. One of these selections
"%s" or "%s"
yielded zero or several atoms. Possible reason for it is the presence of
insertion codes or alternative conformations for one of these residues or
the .pdb file was edited without updating SHEET records.""" \
% (curr_strand.bond_start_current, curr_strand.bond_start_previous)
raise Sorry(error_msg)
current_start_res_is_donor = pdb_hierarchy.atoms().select(
curr_start)[0].name.strip() == 'N'
if (len_curr_residues > 0) and (len_prev_residues > 0):
i = _find_start_residue(residues=prev_rgs,
start_selection=prev_start)
j = _find_start_residue(residues=curr_rgs,
start_selection=curr_start)
if (i >= 0) and (j >= 0):
# move i,j pointers from registration residues to the beginning of
# beta-strands
while (1 < i
and ((1 < j and curr_strand.sense == "parallel") or
(j < len_curr_residues - 2
and curr_strand.sense == "antiparallel"))):
if curr_strand.sense == "parallel":
i -= 2
j -= 2
elif curr_strand.sense == "antiparallel":
i -= 2
j += 2
if (curr_strand.sense == "parallel"):
# some tweaking for ensure correct donor assignment
if i >= 2 and not current_start_res_is_donor:
i -= 2
current_start_res_is_donor = not current_start_res_is_donor
if j >= 2 and current_start_res_is_donor:
j -= 2
current_start_res_is_donor = not current_start_res_is_donor
while (i < len_prev_residues) and (j <
len_curr_residues):
prev_atoms = None
if current_start_res_is_donor:
donor_residue = curr_rgs[j]
if j > 0:
prev_atoms = curr_rgs[j - 1].atoms()
acceptor_residue = prev_rgs[i]
i += 2
else:
donor_residue = prev_rgs[i]
if i > 0:
prev_atoms = prev_rgs[i - 1].atoms()
acceptor_residue = curr_rgs[j]
j += 2
current_start_res_is_donor = not current_start_res_is_donor
if donor_residue.atom_groups()[0].resname.strip(
) != "PRO":
proxies, angle_proxies = _create_hbond_proxy(
acceptor_atoms=acceptor_residue.atoms(),
donor_atoms=donor_residue.atoms(),
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
prev_atoms=prev_atoms,
angle_restraint_type=angle_restraint_type,
weight=weight,
sigma=sheet_params.sigma,
slack=sheet_params.slack,
top_out=sheet_params.top_out,
angle_sigma_scale=sheet_params.
angle_sigma_scale,
angle_sigma_set=sheet_params.
angle_sigma_set,
log=log)
for proxy in proxies:
generated_proxies.append(proxy)
hb_angle_proxies += angle_proxies
elif (curr_strand.sense == "antiparallel"):
while (i < len_prev_residues and j >= 0):
prev_atoms = None
if (prev_rgs[i].atom_groups()[0].resname.strip() !=
"PRO"):
if i > 0:
prev_atoms = prev_rgs[i - 1].atoms()
proxies, angle_proxies = _create_hbond_proxy(
acceptor_atoms=curr_rgs[j].atoms(),
donor_atoms=prev_rgs[i].atoms(),
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
prev_atoms=prev_atoms,
angle_restraint_type=angle_restraint_type,
weight=weight,
sigma=sheet_params.sigma,
slack=sheet_params.slack,
top_out=sheet_params.top_out,
angle_sigma_scale=sheet_params.
angle_sigma_scale,
angle_sigma_set=sheet_params.
angle_sigma_set,
log=log)
for proxy in proxies:
generated_proxies.append(proxy)
hb_angle_proxies += angle_proxies
prev_atoms = None
if (curr_rgs[j].atom_groups()[0].resname.strip() !=
"PRO"):
if j > 0:
prev_atoms = curr_rgs[j - 1].atoms()
proxies, angle_proxies = _create_hbond_proxy(
acceptor_atoms=prev_rgs[i].atoms(),
donor_atoms=curr_rgs[j].atoms(),
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
prev_atoms=prev_atoms,
angle_restraint_type=angle_restraint_type,
weight=weight,
sigma=sheet_params.sigma,
slack=sheet_params.slack,
top_out=sheet_params.top_out,
angle_sigma_scale=sheet_params.
angle_sigma_scale,
angle_sigma_set=sheet_params.
angle_sigma_set,
log=log)
for proxy in proxies:
generated_proxies.append(proxy)
hb_angle_proxies += angle_proxies
i += 2
j -= 2
else:
print(" WARNING: strand direction not defined!",
file=log)
print(" previous: %s" % prev_strand, file=log)
print(" current: %s" % curr_strand.selection,
file=log)
else:
print(
" WARNING: can't find start of bonding for strands!",
file=log)
print(" previous: %s" % prev_strand, file=log)
print(" current: %s" % curr_strand.selection, file=log)
else:
print(" WARNING: can't find one or more strands!", file=log)
print(" previous: %s" % prev_strand, file=log)
print(" current: %s" % curr_strand.selection, file=log)
k += 1
prev_strand = curr_strand.selection
prev_selection = curr_selection
prev_rgs = curr_rgs
return generated_proxies, hb_angle_proxies
def create_helix_hydrogen_bond_proxies(params,
pdb_hierarchy,
selection_cache,
weight,
hbond_counts,
distance_ideal,
distance_cut,
remove_outliers,
restrain_hbond_angles,
log=sys.stdout):
assert (not None in [distance_ideal, distance_cut])
generated_proxies = geometry_restraints.shared_bond_simple_proxy()
hb_angle_proxies = []
helix_class = params.helix_type
if helix_class == "alpha":
helix_step = 4
elif helix_class == "pi":
helix_step = 5
elif helix_class == "3_10":
helix_step = 3
else:
print(" Don't know bonding for helix class %s." % helix_class,
file=log)
return generated_proxies, hb_angle_proxies
try:
helix_selection = selection_cache.selection(params.selection)
except Exception as e:
print(str(e), file=log)
return generated_proxies, hb_angle_proxies
assert (helix_step in [3, 4, 5])
helix_rgs = _get_residue_groups_from_selection(pdb_hierarchy,
helix_selection)
i = 0
just_after_pro = False
while i < len(helix_rgs) - helix_step:
if helix_rgs[i + helix_step].atom_groups()[0].resname.strip() == "PRO":
print(" Proline residue: %s - end of helix" % \
(helix_rgs[i+helix_step].id_str()), file=log)
i += 3
just_after_pro = True
continue # XXX is this safe?
angle_restraint_type = 0
if restrain_hbond_angles and helix_class == "alpha":
if i == 0 or i == len(
helix_rgs) - helix_step - 1 or just_after_pro:
angle_restraint_type = 1
just_after_pro = False
else:
angle_restraint_type = 2
proxies, angle_proxies = _create_hbond_proxy(
acceptor_atoms=helix_rgs[i].atoms(),
donor_atoms=helix_rgs[i + helix_step].atoms(),
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
prev_atoms=helix_rgs[i + helix_step - 1].atoms(),
angle_restraint_type=angle_restraint_type,
weight=weight,
sigma=params.sigma,
slack=params.slack,
angle_sigma_scale=params.angle_sigma_scale,
angle_sigma_set=params.angle_sigma_set,
log=log)
for proxy in proxies:
generated_proxies.append(proxy)
hb_angle_proxies += angle_proxies
i += 1
return generated_proxies, hb_angle_proxies
def exercise_restrained_refinement(options):
import random
random.seed(1)
flex.set_random_seed(1)
xs0 = smtbx.development.random_xray_structure(
sgtbx.space_group_info('P1'),
n_scatterers=options.n_scatterers,
elements="random")
for sc in xs0.scatterers():
sc.flags.set_grad_site(True)
sc0 = xs0.scatterers()
uc = xs0.unit_cell()
mi = xs0.build_miller_set(anomalous_flag=False, d_min=options.resolution)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
i, j, k, l = random.sample(xrange(options.n_scatterers), 4)
bond_proxies = geometry_restraints.shared_bond_simple_proxy()
w = 1e9
d_ij = uc.distance(sc0[i].site, sc0[j].site) * 0.8
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(i, j), distance_ideal=d_ij, weight=w))
d_jk = uc.distance(sc0[j].site, sc0[k].site) * 0.85
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(j, k), distance_ideal=d_jk, weight=w))
d_ki = min(
uc.distance(sc0[k].site, sc0[i].site) * 0.9, (d_ij + d_jk) * 0.8)
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(k, i), distance_ideal=d_ki, weight=w))
d_jl = uc.distance(sc0[j].site, sc0[l].site) * 0.9
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(j, l), distance_ideal=d_jl, weight=w))
d_lk = min(
uc.distance(sc0[l].site, sc0[k].site) * 0.8, 0.75 * (d_jk + d_jl))
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(l, k), distance_ideal=d_jl, weight=w))
restraints_manager = restraints.manager(bond_proxies=bond_proxies)
xs1 = xs0.deep_copy_scatterers()
xs1.shake_sites_in_place(rms_difference=0.1)
def ls_problem():
xs = xs1.deep_copy_scatterers()
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=smtbx.utils.connectivity_table(xs),
temperature=20)
return least_squares.crystallographic_ls(
fo_sq.as_xray_observations(),
reparametrisation=reparametrisation,
restraints_manager=restraints_manager)
gradient_threshold, step_threshold = 1e-6, 1e-6
eps = 5e-3
ls = ls_problem()
t = wall_clock_time()
cycles = normal_eqns_solving.naive_iterations(
ls,
gradient_threshold=gradient_threshold,
step_threshold=step_threshold,
track_all=True)
if options.verbose:
print "%i %s steps in %.6f s" % (cycles.n_iterations, cycles,
t.elapsed())
sc = ls.xray_structure.scatterers()
for p in bond_proxies:
d = uc.distance(*[sc[i_pair].site for i_pair in p.i_seqs])
assert approx_equal(d, p.distance_ideal, eps)
ls = ls_problem()
t = wall_clock_time()
cycles = normal_eqns_solving.levenberg_marquardt_iterations(
ls,
gradient_threshold=gradient_threshold,
step_threshold=step_threshold,
tau=1e-3,
track_all=True)
if options.verbose:
print "%i %s steps in %.6f s" % (cycles.n_iterations, cycles,
t.elapsed())
sc = ls.xray_structure.scatterers()
sc = ls.xray_structure.scatterers()
for p in bond_proxies:
d = uc.distance(*[sc[i].site for i in p.i_seqs])
assert approx_equal(d, p.distance_ideal, eps)
def exercise_geometry_restraints_as_cif():
quartz = xray.structure(crystal_symmetry=crystal.symmetry(
(5.01, 5.01, 5.47, 90, 90, 120), "P6222"),
scatterers=flex.xray_scatterer([
xray.scatterer("Si", (1 / 2., 1 / 2., 1 / 3.)),
xray.scatterer("O", (0.197, -0.197, 0.83333))
]))
bond_proxies = geometry_restraints.shared_bond_simple_proxy((
geometry_restraints.bond_simple_proxy(
i_seqs=[0, 1],
rt_mx_ji=sgtbx.rt_mx("x-y,x,z-2/3"),
distance_ideal=1.6,
weight=3.2),
geometry_restraints.bond_simple_proxy(i_seqs=[0, 1],
distance_ideal=1.7,
weight=1.8),
))
dihedral_proxies = geometry_restraints.shared_dihedral_proxy((
geometry_restraints.dihedral_proxy(
i_seqs=[1, 0, 1, 0],
sym_ops=(sgtbx.rt_mx("1+y,1-x+y, z-1/3"), sgtbx.rt_mx(),
sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx("1-x,y-x,1/3-z")),
angle_ideal=-30,
weight=2),
geometry_restraints.dihedral_proxy(
i_seqs=[1, 0, 1, 0],
sym_ops=(sgtbx.rt_mx("1+y,1-x+y, z-1/3"), sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3"), sgtbx.rt_mx("x-y,x,1/3+z")),
angle_ideal=90,
weight=3),
))
angle_proxies = geometry_restraints.shared_angle_proxy((
geometry_restraints.angle_proxy(i_seqs=[1, 0, 1],
sym_ops=(sgtbx.rt_mx("x-y,x,z-2/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3")),
angle_ideal=103,
weight=2),
geometry_restraints.angle_proxy(
i_seqs=[1, 0, 1],
sym_ops=(sgtbx.rt_mx("y+1,-x+y+1,z-1/3"), sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3")),
angle_ideal=110,
weight=5),
geometry_restraints.angle_proxy(i_seqs=[0, 1, 0],
sym_ops=(sgtbx.rt_mx("y,-x+y,z+2/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-x+y,-x,z+1/3")),
angle_ideal=150,
weight=5),
))
bond_similarity_proxies = geometry_restraints.shared_bond_similarity_proxy(
(geometry_restraints.bond_similarity_proxy(
i_seqs=[(0, 1), (0, 1), (0, 1)],
sym_ops=(sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx("-y,x-y,z-1/3"),
sgtbx.rt_mx("y+1,-x+y+1,z-1/3")),
weights=(1, 1, 1)), ))
cif_block = iotbx.cif.model.block()
iotbx.cif.restraints.add_to_cif_block(
cif_block,
quartz,
bond_proxies=bond_proxies,
angle_proxies=angle_proxies,
dihedral_proxies=dihedral_proxies,
bond_similarity_proxies=bond_similarity_proxies)
s = StringIO()
cif_block.show(out=s)
assert not show_diff(
s.getvalue(), """\
loop_
_restr_distance_atom_site_label_1
_restr_distance_atom_site_label_2
_restr_distance_site_symmetry_2
_restr_distance_target
_restr_distance_target_weight_param
_restr_distance_diff
Si O 2_554 1.6000 0.5590 -0.0160
Si O 1 1.7000 0.7454 -2.3838
loop_
_restr_angle_atom_site_label_1
_restr_angle_atom_site_label_2
_restr_angle_atom_site_label_3
_restr_angle_site_symmetry_1
_restr_angle_site_symmetry_2
_restr_angle_site_symmetry_3
_restr_angle_target
_restr_angle_target_weight_param
_restr_angle_diff
O Si O 2_554 1 4_554 103.0000 0.7071 1.6926
O Si O 3_664 1 4_554 110.0000 0.4472 -1.3127
Si O Si 3 1 5 150.0000 0.4472 3.0700
loop_
_restr_torsion_atom_site_label_1
_restr_torsion_atom_site_label_2
_restr_torsion_atom_site_label_3
_restr_torsion_atom_site_label_4
_restr_torsion_site_symmetry_1
_restr_torsion_site_symmetry_2
_restr_torsion_site_symmetry_3
_restr_torsion_site_symmetry_4
_restr_torsion_angle_target
_restr_torsion_weight_param
_restr_torsion_diff
O Si O Si 3_664 1 2_554 7_655 -30.0000 0.7071 6.9078
O Si O Si 3_664 1 4_554 2 90.0000 0.5774 11.7036
loop_
_restr_equal_distance_class_class_id
_restr_equal_distance_class_target_weight_param
_restr_equal_distance_class_average
_restr_equal_distance_class_esd
_restr_equal_distance_class_diff_max
1 1.0000 1.6160 0.0000 0.0000
loop_
_restr_equal_distance_atom_site_label_1
_restr_equal_distance_atom_site_label_2
_restr_equal_distance_site_symmetry_2
_restr_equal_distance_class_id
Si O 2_554 1
Si O 4_554 1
Si O 3_664 1
""")
def exercise_geometry_restraints_as_cif():
quartz = xray.structure(
crystal_symmetry=crystal.symmetry(
(5.01,5.01,5.47,90,90,120), "P6222"),
scatterers=flex.xray_scatterer([
xray.scatterer("Si", (1/2.,1/2.,1/3.)),
xray.scatterer("O", (0.197,-0.197,0.83333))]))
bond_proxies = geometry_restraints.shared_bond_simple_proxy((
geometry_restraints.bond_simple_proxy(
i_seqs=[0,1],
rt_mx_ji=sgtbx.rt_mx("x-y,x,z-2/3"),
distance_ideal=1.6,
weight=3.2),
geometry_restraints.bond_simple_proxy(
i_seqs=[0,1],
distance_ideal=1.7,
weight=1.8),
))
dihedral_proxies = geometry_restraints.shared_dihedral_proxy((
geometry_restraints.dihedral_proxy(
i_seqs = [1,0,1,0],
sym_ops = (sgtbx.rt_mx("1+y,1-x+y, z-1/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("x-y,x,z-2/3"),
sgtbx.rt_mx("1-x,y-x,1/3-z")),
angle_ideal=-30,
weight=2),
geometry_restraints.dihedral_proxy(
i_seqs = [1,0,1,0],
sym_ops = (sgtbx.rt_mx("1+y,1-x+y, z-1/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3"),
sgtbx.rt_mx("x-y,x,1/3+z")),
angle_ideal=90,
weight=3),
))
angle_proxies = geometry_restraints.shared_angle_proxy((
geometry_restraints.angle_proxy(
i_seqs = [1,0,1],
sym_ops = (sgtbx.rt_mx("x-y,x,z-2/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3")),
angle_ideal=103,
weight=2),
geometry_restraints.angle_proxy(
i_seqs = [1,0,1],
sym_ops = (sgtbx.rt_mx("y+1,-x+y+1,z-1/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3")),
angle_ideal=110,
weight=5),
geometry_restraints.angle_proxy(
i_seqs = [0,1,0],
sym_ops = (sgtbx.rt_mx("y,-x+y,z+2/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-x+y,-x,z+1/3")),
angle_ideal=150,
weight=5),
))
bond_similarity_proxies = geometry_restraints.shared_bond_similarity_proxy((
geometry_restraints.bond_similarity_proxy(
i_seqs=[(0,1),(0,1),(0,1)],
sym_ops=(sgtbx.rt_mx("x-y,x,z-2/3"),
sgtbx.rt_mx("-y,x-y,z-1/3"),
sgtbx.rt_mx("y+1,-x+y+1,z-1/3")),
weights=(1,1,1)),
))
cif_block = iotbx.cif.model.block()
iotbx.cif.restraints.add_to_cif_block(
cif_block, quartz,
bond_proxies=bond_proxies,
angle_proxies=angle_proxies,
dihedral_proxies=dihedral_proxies,
bond_similarity_proxies=bond_similarity_proxies)
s = StringIO()
cif_block.show(out=s)
assert not show_diff(s.getvalue(), """\
loop_
_restr_distance_atom_site_label_1
_restr_distance_atom_site_label_2
_restr_distance_site_symmetry_2
_restr_distance_target
_restr_distance_target_weight_param
_restr_distance_diff
Si O 2_554 1.6000 0.5590 -0.0160
Si O 1 1.7000 0.7454 -2.3838
loop_
_restr_angle_atom_site_label_1
_restr_angle_atom_site_label_2
_restr_angle_atom_site_label_3
_restr_angle_site_symmetry_1
_restr_angle_site_symmetry_2
_restr_angle_site_symmetry_3
_restr_angle_target
_restr_angle_target_weight_param
_restr_angle_diff
O Si O 2_554 1 4_554 103.0000 0.7071 1.6926
O Si O 3_664 1 4_554 110.0000 0.4472 -1.3127
Si O Si 3 1 5 150.0000 0.4472 3.0700
loop_
_restr_torsion_atom_site_label_1
_restr_torsion_atom_site_label_2
_restr_torsion_atom_site_label_3
_restr_torsion_atom_site_label_4
_restr_torsion_site_symmetry_1
_restr_torsion_site_symmetry_2
_restr_torsion_site_symmetry_3
_restr_torsion_site_symmetry_4
_restr_torsion_angle_target
_restr_torsion_weight_param
_restr_torsion_diff
O Si O Si 3_664 1 2_554 7_655 -30.0000 0.7071 6.9078
O Si O Si 3_664 1 4_554 2 90.0000 0.5774 11.7036
loop_
_restr_equal_distance_class_class_id
_restr_equal_distance_class_target_weight_param
_restr_equal_distance_class_average
_restr_equal_distance_class_esd
_restr_equal_distance_class_diff_max
1 1.0000 1.6160 0.0000 0.0000
loop_
_restr_equal_distance_atom_site_label_1
_restr_equal_distance_atom_site_label_2
_restr_equal_distance_site_symmetry_2
_restr_equal_distance_class_id
Si O 2_554 1
Si O 4_554 1
Si O 3_664 1
""")
def create_sheet_hydrogen_bond_proxies (
sheet_params,
pdb_hierarchy,
weight,
hbond_counts,
distance_ideal,
distance_cut,
remove_outliers,
log=sys.stdout) :
assert (not None in [distance_ideal, distance_cut])
cache = pdb_hierarchy.atom_selection_cache()
prev_strand = sheet_params.first_strand
prev_selection = cache.selection(prev_strand)
prev_rgs = _get_residue_groups_from_selection(
pdb_hierarchy=pdb_hierarchy,
bool_selection=prev_selection)
n_proxies = 0
k = 0
generated_proxies = geometry_restraints.shared_bond_simple_proxy()
while k < len(sheet_params.strand) :
curr_strand = sheet_params.strand[k]
curr_selection = cache.selection(curr_strand.selection)
curr_start = None
prev_start = None
if curr_strand.bond_start_current is not None:
curr_start = cache.selection(curr_strand.bond_start_current)
if curr_strand.bond_start_previous is not None:
prev_start = cache.selection(curr_strand.bond_start_previous)
curr_rgs = _get_residue_groups_from_selection(
pdb_hierarchy=pdb_hierarchy,
bool_selection=curr_selection)
i = j = 0
len_prev_residues = len(prev_rgs)
len_curr_residues = len(curr_rgs)
if curr_start is not None and prev_start is not None:
if curr_start.count(True) < 1 or prev_start.count(True) < 1:
error_msg = """\
Wrong registration in SHEET record. One of these selections
"%s" or "%s"
yielded zero or several atoms. Possible reason for it is the presence of
insertion codes or alternative conformations for one of these residues or
the .pdb file was edited without updating SHEET records.""" \
% (curr_strand.bond_start_current, curr_strand.bond_start_previous)
raise Sorry(error_msg)
current_start_res_is_donor = pdb_hierarchy.atoms().select(curr_start)[0].name.strip() == 'N'
if (len_curr_residues > 0) and (len_prev_residues > 0) :
i = _find_start_residue(
residues=prev_rgs,
start_selection=prev_start)
j = _find_start_residue(
residues=curr_rgs,
start_selection=curr_start)
if (i >= 0) and (j >= 0) :
# move i,j pointers from registration residues to the beginning of
# beta-strands
while (1 < i and
((1 < j and curr_strand.sense == "parallel") or
(j < len_curr_residues-2 and curr_strand.sense == "antiparallel"))):
if curr_strand.sense == "parallel":
i -= 2
j -= 2
elif curr_strand.sense == "antiparallel":
i -= 2
j += 2
if (curr_strand.sense == "parallel") :
# some tweaking for ensure correct donor assignment
if i >= 2 and not current_start_res_is_donor:
i -= 2
current_start_res_is_donor = not current_start_res_is_donor
if j >= 2 and current_start_res_is_donor:
j -= 2
current_start_res_is_donor = not current_start_res_is_donor
while (i < len_prev_residues) and (j < len_curr_residues):
if current_start_res_is_donor:
donor_residue = curr_rgs[j]
acceptor_residue = prev_rgs[i]
i += 2
else:
donor_residue = prev_rgs[i]
acceptor_residue = curr_rgs[j]
j += 2
current_start_res_is_donor = not current_start_res_is_donor
if donor_residue.atom_groups()[0].resname.strip() != "PRO":
proxies = _create_hbond_proxy(
acceptor_atoms=acceptor_residue.atoms(),
donor_atoms=donor_residue.atoms(),
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
weight=weight,
sigma=sheet_params.sigma,
slack=sheet_params.slack,
top_out=sheet_params.top_out,
log=log)
if proxies is not None:
for proxy in proxies:
generated_proxies.append(proxy)
elif (curr_strand.sense == "antiparallel") :
while(i < len_prev_residues and j >= 0):
if (prev_rgs[i].atom_groups()[0].resname.strip() != "PRO") :
proxies = _create_hbond_proxy(
acceptor_atoms=curr_rgs[j].atoms(),
donor_atoms=prev_rgs[i].atoms(),
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
weight=weight,
sigma=sheet_params.sigma,
slack=sheet_params.slack,
top_out=sheet_params.top_out,
log=log)
if proxies is not None:
for proxy in proxies:
generated_proxies.append(proxy)
if (curr_rgs[j].atom_groups()[0].resname.strip() != "PRO") :
proxies = _create_hbond_proxy(
acceptor_atoms=prev_rgs[i].atoms(),
donor_atoms=curr_rgs[j].atoms(),
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
weight=weight,
sigma=sheet_params.sigma,
slack=sheet_params.slack,
top_out=sheet_params.top_out,
log=log)
if proxies is not None:
for proxy in proxies:
generated_proxies.append(proxy)
i += 2;
j -= 2;
else :
print >> log, " WARNING: strand direction not defined!"
print >> log, " previous: %s" % prev_strand
print >> log, " current: %s" % curr_strand.selection
else :
print >> log, " WARNING: can't find start of bonding for strands!"
print >> log, " previous: %s" % prev_strand
print >> log, " current: %s" % curr_strand.selection
else :
print >> log, " WARNING: can't find one or more strands!"
print >> log, " previous: %s" % prev_strand
print >> log, " current: %s" % curr_strand.selection
k += 1
prev_strand = curr_strand.selection
prev_selection = curr_selection
prev_rgs = curr_rgs
return generated_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)
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 exercise_restrained_refinement(options):
import random
random.seed(1)
flex.set_random_seed(1)
xs0 = smtbx.development.random_xray_structure(
sgtbx.space_group_info('P1'),
n_scatterers=options.n_scatterers,
elements="random")
for sc in xs0.scatterers():
sc.flags.set_grad_site(True)
sc0 = xs0.scatterers()
uc = xs0.unit_cell()
mi = xs0.build_miller_set(anomalous_flag=False, d_min=options.resolution)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
i, j, k, l = random.sample(xrange(options.n_scatterers), 4)
bond_proxies = geometry_restraints.shared_bond_simple_proxy()
w = 1e9
d_ij = uc.distance(sc0[i].site, sc0[j].site)*0.8
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(i, j),
distance_ideal=d_ij,
weight=w))
d_jk = uc.distance(sc0[j].site, sc0[k].site)*0.85
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(j, k),
distance_ideal=d_jk,
weight=w))
d_ki = min(uc.distance(sc0[k].site, sc0[i].site)*0.9, (d_ij + d_jk)*0.8)
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(k, i),
distance_ideal=d_ki,
weight=w))
d_jl = uc.distance(sc0[j].site, sc0[l].site)*0.9
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(j, l),
distance_ideal=d_jl,
weight=w))
d_lk = min(uc.distance(sc0[l].site, sc0[k].site)*0.8, 0.75*(d_jk + d_jl))
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(l, k),
distance_ideal=d_jl,
weight=w))
restraints_manager = restraints.manager(bond_proxies=bond_proxies)
xs1 = xs0.deep_copy_scatterers()
xs1.shake_sites_in_place(rms_difference=0.1)
def ls_problem():
xs = xs1.deep_copy_scatterers()
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=smtbx.utils.connectivity_table(xs),
temperature=20)
return least_squares.crystallographic_ls(
fo_sq.as_xray_observations(),
reparametrisation=reparametrisation,
restraints_manager=restraints_manager)
gradient_threshold, step_threshold = 1e-6, 1e-6
eps = 5e-3
ls = ls_problem()
t = wall_clock_time()
cycles = normal_eqns_solving.naive_iterations(
ls,
gradient_threshold=gradient_threshold,
step_threshold=step_threshold,
track_all=True)
if options.verbose:
print "%i %s steps in %.6f s" % (cycles.n_iterations, cycles, t.elapsed())
sc = ls.xray_structure.scatterers()
for p in bond_proxies:
d = uc.distance(*[ sc[i_pair].site for i_pair in p.i_seqs ])
assert approx_equal(d, p.distance_ideal, eps)
ls = ls_problem()
t = wall_clock_time()
cycles = normal_eqns_solving.levenberg_marquardt_iterations(
ls,
gradient_threshold=gradient_threshold,
step_threshold=step_threshold,
tau=1e-3,
track_all=True)
if options.verbose:
print "%i %s steps in %.6f s" % (cycles.n_iterations, cycles, t.elapsed())
sc = ls.xray_structure.scatterers()
sc = ls.xray_structure.scatterers()
for p in bond_proxies:
d = uc.distance(*[ sc[i].site for i in p.i_seqs ])
assert approx_equal(d, p.distance_ideal, eps)
def get_basepair_hbond_proxies(pdb_hierarchy,
bp_phil_params,
hbond_distance_cutoff=3.4):
assert pdb_hierarchy is not None
bond_proxies_result = []
angle_proxies_result = []
if len(bp_phil_params) > 0:
# return bond_proxies_result, angle_proxies_result
selection_cache = pdb_hierarchy.atom_selection_cache()
pdb_atoms = pdb_hierarchy.atoms()
# dashes = open('dashes.pml', 'w')
pdb_atoms = pdb_hierarchy.atoms()
for base_pair in bp_phil_params:
if (base_pair.base1 is not None and base_pair.base2 is not None
and base_pair.enabled):
selected_atoms_1 = selection_cache.iselection(base_pair.base1)
selected_atoms_2 = selection_cache.iselection(base_pair.base2)
if len(selected_atoms_1) == 0:
raise Sorry(
"Selection %s in base_pair retusulted in 0 atoms." %
(base_pair.base1))
if len(selected_atoms_2) == 0:
raise Sorry(
"Selection %s in base_pair retusulted in 0 atoms." %
(base_pair.base2))
a1 = pdb_atoms[selected_atoms_1[0]]
a2 = pdb_atoms[selected_atoms_2[0]]
if base_pair.saenger_class == 0:
hbonds, saenger_class = get_h_bonds_for_basepair(
a1,
a2,
distance_cutoff=hbond_distance_cutoff,
log=sys.stdout,
verbose=-1)
base_pair.saenger_class = saenger_class
hbonds = get_h_bonds_for_particular_basepair(
(a1, a2), base_pair.saenger_class)
for hb in hbonds:
if hb[0] is None or hb[1] is None:
print "NA hbond rejected because one of the atoms is absent"
continue
dist = hb[0].distance(hb[1])
if dist < hbond_distance_cutoff:
if base_pair.restrain_hbonds:
hb_target, hb_sigma = get_hb_lenght_targets(hb)
p = geometry_restraints.bond_simple_proxy(
i_seqs=[hb[0].i_seq, hb[1].i_seq],
distance_ideal=hb_target,
weight=1.0 / hb_sigma**2,
slack=0,
top_out=False,
limit=1,
origin_id=1)
bond_proxies_result.append(p)
# print "bond:", hb[0].id_str(), hb[1].id_str(), "(%4.2f, %4.2f)" % (hb_target, hb_sigma)
# s1 = pdb_atoms[hb[0].i_seq].id_str()
# s2 = pdb_atoms[hb[1].i_seq].id_str()
# ps = "dist chain \"%s\" and resi %s and name %s, chain \"%s\" and resi %s and name %s\n" % (
# s1[14:15], s1[15:19], s1[5:8], s2[14:15], s2[15:19], s2[5:8])
# dashes.write(ps)
if base_pair.restrain_hb_angles:
angle_proxies_result += get_angle_proxies_for_bond(
hb)
else:
print "NA hbond rejected:", hb[0].id_str(
), hb[1].id_str(), "distance=%.2f" % dist
# dashes.close()
return geometry_restraints.shared_bond_simple_proxy(bond_proxies_result), \
angle_proxies_result
