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(),
}
class angle_restraint_test_case(geometry_restraints_test_case):
manager = restraints.manager(
angle_proxies=geometry_restraints.shared_angle_proxy([
geom.angle_proxy((30, 0, 19), 115, 1),
geom.angle_proxy((21, 1, 2), 110, 1)
]))
proxies = manager.angle_proxies
restraint_t = geom.angle
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)
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(verbose=0):
distance_ideal = 1.8
default_vdw_distance = 3.6
vdw_1_4_factor = 3.5 / 3.6
sites_cart_manual = flex.vec3_double([(1, 3, 0), (2, 3, 0), (3, 2, 0),
(3, 1, 0), (4, 1, 0), (3, 4, 0),
(4, 3, 0), (5, 3, 0), (6, 2, 0),
(7, 2, 0), (8, 3, 0), (7, 4, 0),
(6, 4, 0), (7, 5, 0), (6, 6, 0),
(8, 6, 0)])
bond_proxies = geometry_restraints.bond_sorted_asu_proxies(
asu_mappings=None)
for i_seqs in [(0, 1), (1, 2), (2, 3), (3, 4), (1, 5), (2, 6), (5, 6),
(6, 7), (7, 8), (8, 9), (9, 10), (10, 11), (11, 12),
(12, 7), (11, 13), (13, 14), (14, 15), (15, 13)]:
bond_proxies.process(
geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs, distance_ideal=distance_ideal, weight=100))
angle_proxies = geometry_restraints.shared_angle_proxy()
for i_seqs, angle_ideal in [[(0, 1, 2), 135], [(0, 1, 5), 135],
[(1, 2, 3), 135], [(3, 2, 6), 135],
[(2, 3, 4), 120], [(1, 2, 6), 90],
[(2, 6, 5), 90], [(6, 5, 1), 90],
[(5, 1, 2), 90], [(2, 6, 7), 135],
[(5, 6, 7), 135], [(6, 7, 8), 120],
[(6, 7, 12), 120], [(7, 8, 9), 120],
[(8, 9, 10), 120], [(9, 10, 11), 120],
[(10, 11, 12), 120], [(11, 12, 7), 120],
[(12, 7, 8), 120], [(10, 11, 13), 120],
[(12, 11, 13), 120], [(11, 13, 15), 150],
[(11, 13, 14), 150], [(13, 15, 14), 60],
[(15, 14, 13), 60], [(14, 13, 15), 60]]:
angle_proxies.append(
geometry_restraints.angle_proxy(i_seqs=i_seqs,
angle_ideal=angle_ideal,
weight=1))
if (0 or verbose):
dump_pdb(file_name="manual.pdb", sites_cart=sites_cart_manual)
for traditional_convergence_test in [True, False]:
for sites_cart_selection in [True, False]:
sites_cart = sites_cart_manual.deep_copy()
if sites_cart_selection:
sites_cart_selection = flex.bool(sites_cart.size(), True)
sites_cart_selection[1] = False
assert bond_proxies.asu.size() == 0
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(),
bond_simple_proxies=bond_proxies.simple)
manager = geometry_restraints.manager.manager(
bond_params_table=bond_params_table,
angle_proxies=angle_proxies)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
traditional_convergence_test=traditional_convergence_test,
drop_convergence_test_max_drop_eps=1.e-20,
drop_convergence_test_iteration_coefficient=1,
max_iterations=1000),
sites_cart_selection=sites_cart_selection,
)
assert minimized.minimizer.iter() > 100
sites_cart_minimized_1 = sites_cart.deep_copy()
if (0 or verbose):
dump_pdb(file_name="minimized_1.pdb",
sites_cart=sites_cart_minimized_1)
bond_deltas = geometry_restraints.bond_deltas(
sites_cart=sites_cart_minimized_1, proxies=bond_proxies.simple)
angle_deltas = geometry_restraints.angle_deltas(
sites_cart=sites_cart_minimized_1, proxies=angle_proxies)
if (0 or verbose):
for proxy, delta in zip(bond_proxies.simple, bond_deltas):
print "bond:", proxy.i_seqs, delta
for proxy, delta in zip(angle_proxies, angle_deltas):
print "angle:", proxy.i_seqs, delta
assert is_below_limit(value=flex.max(flex.abs(bond_deltas)),
limit=0,
eps=1.e-6)
assert is_below_limit(value=flex.max(flex.abs(angle_deltas)),
limit=0,
eps=2.e-6)
sites_cart += matrix.col((1, 1, 0)) - matrix.col(sites_cart.min())
unit_cell_lengths = list(
matrix.col(sites_cart.max()) + matrix.col((1, -1.2, 4)))
unit_cell_lengths[1] *= 2
unit_cell_lengths[2] *= 2
xray_structure = xray.structure(crystal_symmetry=crystal.symmetry(
unit_cell=unit_cell_lengths, space_group_symbol="P112"))
for serial, site in zip(count(1), sites_cart):
xray_structure.add_scatterer(
xray.scatterer(
label="C%02d" % serial,
site=xray_structure.unit_cell().fractionalize(site)))
if (0 or verbose):
xray_structure.show_summary().show_scatterers()
p1_structure = (xray_structure.apply_shift(
(-.5, -.5, 0)).expand_to_p1().apply_shift((.5, .5, 0)))
for shift in [(1, 0, 0), (0, 1, 0), (0, 0, 1)]:
p1_structure.add_scatterers(
p1_structure.apply_shift(shift).scatterers())
if (0 or verbose):
open("p1_structure.pdb", "w").write(p1_structure.as_pdb_file())
nonbonded_cutoff = 6.5
asu_mappings = xray_structure.asu_mappings(
buffer_thickness=nonbonded_cutoff)
bond_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
geometry_restraints.add_pairs(bond_asu_table, bond_proxies.simple)
shell_asu_tables = crystal.coordination_sequences.shell_asu_tables(
pair_asu_table=bond_asu_table, max_shell=3)
shell_sym_tables = [
shell_asu_table.extract_pair_sym_table()
for shell_asu_table in shell_asu_tables
]
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(), bond_simple_proxies=bond_proxies.simple)
atom_energy_types = flex.std_string(sites_cart.size(), "Default")
nonbonded_params = geometry_restraints.nonbonded_params(
factor_1_4_interactions=vdw_1_4_factor,
const_shrink_1_4_interactions=0,
default_distance=default_vdw_distance)
nonbonded_params.distance_table.setdefault(
"Default")["Default"] = default_vdw_distance
pair_proxies = geometry_restraints.pair_proxies(
bond_params_table=bond_params_table,
shell_asu_tables=shell_asu_tables,
model_indices=None,
conformer_indices=None,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_distance_cutoff_plus_buffer=nonbonded_cutoff)
if (0 or verbose):
print "pair_proxies.bond_proxies.n_total():", \
pair_proxies.bond_proxies.n_total(),
print "simple:", pair_proxies.bond_proxies.simple.size(),
print "sym:", pair_proxies.bond_proxies.asu.size()
print "pair_proxies.nonbonded_proxies.n_total():", \
pair_proxies.nonbonded_proxies.n_total(),
print "simple:", pair_proxies.nonbonded_proxies.simple.size(),
print "sym:", pair_proxies.nonbonded_proxies.asu.size()
print "min_distance_nonbonded: %.2f" % flex.min(
geometry_restraints.nonbonded_deltas(
sites_cart=sites_cart,
sorted_asu_proxies=pair_proxies.nonbonded_proxies))
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart, f=s, prefix="[]")
assert s.getvalue().splitlines()[0] == "[]Histogram of bond lengths:"
assert s.getvalue().splitlines()[5].startswith("[] 1.80 - 1.80:")
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_deltas(sites_cart=sites_cart,
f=s,
prefix="][")
assert s.getvalue().splitlines()[0] == "][Histogram of bond deltas:"
assert s.getvalue().splitlines()[5].startswith("][ 0.000 - 0.000:")
s = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
max_items=3,
f=s,
prefix=":;")
l = s.getvalue().splitlines()
assert l[0] == ":;Bond restraints: 18"
assert l[1] == ":;Sorted by residual:"
assert l[2].startswith(":;bond ")
assert l[3].startswith(":; ")
assert l[4] == ":; ideal model delta sigma weight residual"
for i in [5, -2]:
assert l[i].startswith(":; 1.800 1.800 ")
assert l[-1] == ":;... (remaining 15 not shown)"
s = StringIO()
pair_proxies.nonbonded_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart, f=s, prefix="]^")
assert not show_diff(
s.getvalue(), """\
]^Histogram of nonbonded interaction distances:
]^ 2.16 - 3.03: 3
]^ 3.03 - 3.89: 12
]^ 3.89 - 4.75: 28
]^ 4.75 - 5.61: 44
]^ 5.61 - 6.48: 54
""")
s = StringIO()
pair_proxies.nonbonded_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
max_items=7,
f=s,
prefix=">,")
assert not show_diff(s.getvalue(),
"""\
>,Nonbonded interactions: 141
>,Sorted by model distance:
>,nonbonded 15
>, 15
>, model vdw sym.op.
>, 2.164 3.600 -x+2,-y+1,z
...
>,nonbonded 4
>, 8
>, model vdw
>, 3.414 3.600
>,... (remaining 134 not shown)
""",
selections=[range(6), range(-5, 0)])
vdw_1_sticks = []
vdw_2_sticks = []
for proxy in pair_proxies.nonbonded_proxies.simple:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(
pml_stick(begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
else:
vdw_2_sticks.append(
pml_stick(begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
mps = asu_mappings.mappings()
for proxy in pair_proxies.nonbonded_proxies.asu:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(
pml_stick(begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
else:
vdw_2_sticks.append(
pml_stick(begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
if (0 or verbose):
pml_write(f=open("vdw_1.pml", "w"), label="vdw_1", sticks=vdw_1_sticks)
pml_write(f=open("vdw_2.pml", "w"), label="vdw_2", sticks=vdw_2_sticks)
#
i_pdb = count(2)
for use_crystal_symmetry in [False, True]:
if (not use_crystal_symmetry):
crystal_symmetry = None
site_symmetry_table = None
else:
crystal_symmetry = xray_structure
site_symmetry_table = xray_structure.site_symmetry_table()
for sites_cart in [
sites_cart_manual.deep_copy(),
sites_cart_minimized_1.deep_copy()
]:
manager = geometry_restraints.manager.manager(
crystal_symmetry=crystal_symmetry,
site_symmetry_table=site_symmetry_table,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_function=geometry_restraints.
prolsq_repulsion_function(),
bond_params_table=bond_params_table,
shell_sym_tables=shell_sym_tables,
nonbonded_distance_cutoff=nonbonded_cutoff,
nonbonded_buffer=1,
angle_proxies=angle_proxies,
plain_pairs_radius=5)
manager = manager.select(
selection=flex.bool(sites_cart.size(), True))
manager = manager.select(iselection=flex.size_t_range(
stop=sites_cart.size()))
pair_proxies = manager.pair_proxies(sites_cart=sites_cart)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=1000))
if (0 or verbose):
minimized.final_target_result.show()
print "number of function evaluations:", minimized.minimizer.nfun(
)
print "n_updates_pair_proxies:", manager.n_updates_pair_proxies
if (not use_crystal_symmetry):
assert minimized.final_target_result.bond_residual_sum < 1.e-3
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
else:
assert minimized.final_target_result.bond_residual_sum < 1.e-2
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
assert minimized.final_target_result.angle_residual_sum < 1.e-3
if (0 or verbose):
pdb_file_name = "minimized_%d.pdb" % i_pdb.next()
print "Writing file:", pdb_file_name
dump_pdb(file_name=pdb_file_name, sites_cart=sites_cart)
if (manager.site_symmetry_table is None):
additional_site_symmetry_table = None
else:
additional_site_symmetry_table = sgtbx.site_symmetry_table()
assert manager.new_including_isolated_sites(
n_additional_sites=0,
site_symmetry_table=additional_site_symmetry_table,
nonbonded_types=flex.std_string()).plain_pairs_radius \
== manager.plain_pairs_radius
if (crystal_symmetry is not None):
assert len(manager.plain_pair_sym_table) == 16
if (0 or verbose):
manager.plain_pair_sym_table.show()
#
xray_structure.set_u_iso(values=flex.double([
0.77599982480241358, 0.38745781137212021, 0.20667558236418682,
0.99759840171302094, 0.8917287406687805, 0.64780251325379845,
0.24878590382983534, 0.59480621182194615, 0.58695637792905142,
0.33997130213653637, 0.51258699130743735, 0.79760289141276675,
0.39996577657875021, 0.4329328819341467, 0.70422156561726479,
0.87260110626999332
]))
class parameters:
pass
parameters.sphere_radius = 5
parameters.distance_power = 0.7
parameters.average_power = 0.9
parameters.wilson_b_weight = 1.3952
parameters.wilson_b_weight_auto = False
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=None,
use_hd=False,
use_u_local_only=False,
compute_gradients=False,
gradients=None,
normalization=False,
collect=True)
assert adp_energies.number_of_restraints == 69
assert approx_equal(adp_energies.residual_sum, 6.24865382467)
assert adp_energies.gradients is None
assert adp_energies.u_i.size() == adp_energies.number_of_restraints
assert adp_energies.u_j.size() == adp_energies.number_of_restraints
assert adp_energies.r_ij.size() == adp_energies.number_of_restraints
for wilson_b in [None, 10, 100]:
finite_difference_gradients = flex.double()
eps = 1.e-6
for i_scatterer in xrange(xray_structure.scatterers().size()):
rs = []
for signed_eps in [eps, -eps]:
xray_structure_eps = xray_structure.deep_copy_scatterers()
xray_structure_eps.scatterers(
)[i_scatterer].u_iso += signed_eps
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure_eps,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only=False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
rs.append(adp_energies.residual_sum)
assert adp_energies.gradients.size() \
== xray_structure.scatterers().size()
assert adp_energies.u_i == None
assert adp_energies.u_j == None
assert adp_energies.r_ij == None
finite_difference_gradients.append((rs[0] - rs[1]) / (2 * eps))
sel = flex.bool(xray_structure.scatterers().size(), True)
xray_structure.scatterers().flags_set_grad_u_iso(sel.iselection())
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only=False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
assert approx_equal(adp_energies.gradients,
finite_difference_gradients)
print "OK"
def read_pdb():
pdbstring = """\
ATOM 0 CA GLY A 3 5.804 -2.100 7.324 1.00 1.36 C
ATOM 1 C GLY A 3 4.651 -1.149 7.578 1.00 1.01 C
ATOM 2 O GLY A 3 3.598 -1.553 8.071 1.00 1.38 O
ATOM 3 N GLY A 3 6.706 -1.622 6.294 1.00 1.11 N
ATOM 4 CA PHE A 4 3.819 1.134 7.419 1.00 0.89 C
ATOM 5 CB PHE A 4 4.397 2.380 8.094 1.00 1.13 C
ATOM 6 C PHE A 4 3.185 1.509 6.084 1.00 0.94 C
ATOM 7 N PHE A 4 4.852 0.121 7.242 1.00 0.88 N
ATOM 8 O PHE A 4 2.361 2.421 6.010 1.00 1.47 O
ATOM 9 CA LEU A 5 3.055 1.059 3.693 1.00 0.87 C
ATOM 10 CB LEU A 5 3.965 0.435 2.634 1.00 1.13 C
ATOM 11 C LEU A 5 1.634 0.527 3.541 1.00 0.87 C
ATOM 12 N LEU A 5 3.576 0.800 5.030 1.00 0.92 N
ATOM 13 O LEU A 5 1.246 -0.440 4.196 1.00 1.23 O
"""
pdb_inp = iotbx.pdb.input(lines=flex.split_lines(pdbstring),
source_info=None)
sites_cart = pdb_inp.atoms().extract_xyz()
# TRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
# TRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
dihedral_proxies = geometry_restraints.shared_dihedral_proxy()
# residue 1
psi = geometry_restraints.dihedral_proxy(i_seqs=[3, 0, 1, 7],
angle_ideal=160.0,
weight=1 / 30.0**2,
periodicity=3)
dihedral_proxies.append(psi)
# residue 2
phi = geometry_restraints.dihedral_proxy(i_seqs=[1, 7, 4, 6],
angle_ideal=60.0,
weight=1 / 20.0**2,
periodicity=3)
dihedral_proxies.append(phi)
psi = geometry_restraints.dihedral_proxy(i_seqs=[7, 4, 6, 8],
angle_ideal=160.0,
weight=1 / 30.0**2,
periodicity=3)
dihedral_proxies.append(psi)
# residue 3
phi = geometry_restraints.dihedral_proxy(i_seqs=[6, 12, 9, 11],
angle_ideal=60.0,
weight=1 / 20.0**2,
periodicity=3)
dihedral_proxies.append(phi)
angle_proxies = geometry_restraints.shared_angle_proxy()
## Residue 1
# a3
a = geometry_restraints.angle_proxy(i_seqs=[3, 0, 1],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# a7
a = geometry_restraints.angle_proxy(i_seqs=[2, 1, 7],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
## Residue 2
# a1
a = geometry_restraints.angle_proxy(i_seqs=[1, 7, 4],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# a3
a = geometry_restraints.angle_proxy(i_seqs=[7, 4, 6],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# a7
a = geometry_restraints.angle_proxy(i_seqs=[8, 6, 12],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
## Residue 3
# a1
a = geometry_restraints.angle_proxy(i_seqs=[6, 12, 9],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# a3
a = geometry_restraints.angle_proxy(i_seqs=[12, 9, 11],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# compute dihedral
#dihedral = geometry_restraints.dihedral(
# sites_cart=sites_cart,
# proxy=dihedral_proxies[0])
# Shows real dihedral value
#print dihedral.angle_model, dihedral.delta
cfd_list = []
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='GLY',
next_residue_name='PHE',
conformation_proxies=None,
i_phi_proxy=None, # index into dihedral_proxies
i_psi_proxy=0,
i_dynamic_angles=[None, None, 0, None, None, None,
1], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None)
cfd_list.append(cfd)
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='PHE',
next_residue_name='LEU',
conformation_proxies=None,
i_phi_proxy=1, # index into dihedral_proxies
i_psi_proxy=2,
i_dynamic_angles=[2, None, 3, None, None, None,
4], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None)
cfd_list.append(cfd)
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='LEU',
next_residue_name=None,
conformation_proxies=None,
i_phi_proxy=3, # index into dihedral_proxies
i_psi_proxy=None,
i_dynamic_angles=[5, None, 6, None, None, None,
None], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None)
cfd_list.append(cfd)
for x in range(1, 4):
print
print 'Starting cycle', x
print
for cfd in cfd_list:
cfd.update_restraints(sites_cart, dihedral_proxies, angle_proxies)
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 read_pdb():
pdbstring = """\
ATOM 0 CA GLY A 3 5.804 -2.100 7.324 1.00 1.36 C
ATOM 1 C GLY A 3 4.651 -1.149 7.578 1.00 1.01 C
ATOM 2 O GLY A 3 3.598 -1.553 8.071 1.00 1.38 O
ATOM 3 N GLY A 3 6.706 -1.622 6.294 1.00 1.11 N
ATOM 4 CA PHE A 4 3.819 1.134 7.419 1.00 0.89 C
ATOM 5 CB PHE A 4 4.397 2.380 8.094 1.00 1.13 C
ATOM 6 C PHE A 4 3.185 1.509 6.084 1.00 0.94 C
ATOM 7 N PHE A 4 4.852 0.121 7.242 1.00 0.88 N
ATOM 8 O PHE A 4 2.361 2.421 6.010 1.00 1.47 O
ATOM 9 CA LEU A 5 3.055 1.059 3.693 1.00 0.87 C
ATOM 10 CB LEU A 5 3.965 0.435 2.634 1.00 1.13 C
ATOM 11 C LEU A 5 1.634 0.527 3.541 1.00 0.87 C
ATOM 12 N LEU A 5 3.576 0.800 5.030 1.00 0.92 N
ATOM 13 O LEU A 5 1.246 -0.440 4.196 1.00 1.23 O
"""
pdb_inp = iotbx.pdb.input(
lines=flex.split_lines(pdbstring), source_info=None)
sites_cart = pdb_inp.atoms().extract_xyz()
# TRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
# TRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
dihedral_proxies = geometry_restraints.shared_dihedral_proxy()
# residue 1
psi = geometry_restraints.dihedral_proxy(
i_seqs=[3, 0, 1, 7],
angle_ideal=160.0,
weight=1/30.0**2,
periodicity=3
)
dihedral_proxies.append(psi)
# residue 2
phi = geometry_restraints.dihedral_proxy(
i_seqs=[1, 7, 4, 6],
angle_ideal=60.0,
weight=1/20.0**2,
periodicity=3
)
dihedral_proxies.append(phi)
psi = geometry_restraints.dihedral_proxy(
i_seqs=[7, 4, 6, 8],
angle_ideal=160.0,
weight=1/30.0**2,
periodicity=3
)
dihedral_proxies.append(psi)
# residue 3
phi = geometry_restraints.dihedral_proxy(
i_seqs=[6, 12, 9, 11],
angle_ideal=60.0,
weight=1/20.0**2,
periodicity=3
)
dihedral_proxies.append(phi)
angle_proxies = geometry_restraints.shared_angle_proxy()
## Residue 1
# a3
a = geometry_restraints.angle_proxy(
i_seqs=[3, 0, 1],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# a7
a = geometry_restraints.angle_proxy(
i_seqs=[2, 1, 7],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
## Residue 2
# a1
a = geometry_restraints.angle_proxy(
i_seqs=[1, 7, 4],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# a3
a = geometry_restraints.angle_proxy(
i_seqs=[7, 4, 6],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# a7
a = geometry_restraints.angle_proxy(
i_seqs=[8, 6, 12],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
## Residue 3
# a1
a = geometry_restraints.angle_proxy(
i_seqs=[6, 12, 9],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# a3
a = geometry_restraints.angle_proxy(
i_seqs=[12, 9, 11],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# compute dihedral
#dihedral = geometry_restraints.dihedral(
# sites_cart=sites_cart,
# proxy=dihedral_proxies[0])
# Shows real dihedral value
#print dihedral.angle_model, dihedral.delta
cfd_list = []
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='GLY',
next_residue_name='PHE',
conformation_proxies=None,
i_phi_proxy=None, # index into dihedral_proxies
i_psi_proxy=0,
i_dynamic_angles=[None, None, 0, None, None, None, 1], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None
)
cfd_list.append(cfd)
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='PHE',
next_residue_name='LEU',
conformation_proxies=None,
i_phi_proxy=1, # index into dihedral_proxies
i_psi_proxy=2,
i_dynamic_angles=[2, None, 3, None, None, None, 4], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None
)
cfd_list.append(cfd)
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='LEU',
next_residue_name=None,
conformation_proxies=None,
i_phi_proxy=3, # index into dihedral_proxies
i_psi_proxy=None,
i_dynamic_angles=[5, None, 6, None, None, None, None], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None
)
cfd_list.append(cfd)
for x in range(1, 4):
print
print 'Starting cycle', x
print
for cfd in cfd_list:
cfd.update_restraints(sites_cart, dihedral_proxies, angle_proxies)
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(verbose=0):
distance_ideal = 1.8
default_vdw_distance = 3.6
vdw_1_4_factor = 3.5/3.6
sites_cart_manual = flex.vec3_double([
(1,3,0), (2,3,0), (3,2,0), (3,1,0), (4,1,0), (3,4,0), (4,3,0), (5,3,0),
(6,2,0), (7,2,0), (8,3,0), (7,4,0), (6,4,0), (7,5,0), (6,6,0), (8,6,0)])
bond_proxies = geometry_restraints.bond_sorted_asu_proxies(asu_mappings=None)
for i_seqs in [(0,1),(1,2),(2,3),(3,4),(1,5),(2,6),(5,6),
(6,7),(7,8),(8,9),(9,10),(10,11),(11,12),
(12,7),(11,13),(13,14),(14,15),(15,13)]:
bond_proxies.process(geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs, distance_ideal=distance_ideal, weight=100))
angle_proxies = geometry_restraints.shared_angle_proxy()
for i_seqs,angle_ideal in [[(0,1,2),135],
[(0,1,5),135],
[(1,2,3),135],
[(3,2,6),135],
[(2,3,4),120],
[(1,2,6),90],
[(2,6,5),90],
[(6,5,1),90],
[(5,1,2),90],
[(2,6,7),135],
[(5,6,7),135],
[(6,7,8),120],
[(6,7,12),120],
[(7,8,9),120],
[(8,9,10),120],
[(9,10,11),120],
[(10,11,12),120],
[(11,12,7),120],
[(12,7,8),120],
[(10,11,13),120],
[(12,11,13),120],
[(11,13,15),150],
[(11,13,14),150],
[(13,15,14),60],
[(15,14,13),60],
[(14,13,15),60]]:
angle_proxies.append(geometry_restraints.angle_proxy(
i_seqs=i_seqs, angle_ideal=angle_ideal, weight=1))
if (0 or verbose):
dump_pdb(file_name="manual.pdb", sites_cart=sites_cart_manual)
for traditional_convergence_test in [True,False]:
for sites_cart_selection in [True, False]:
sites_cart = sites_cart_manual.deep_copy()
if sites_cart_selection:
sites_cart_selection = flex.bool(sites_cart.size(), True)
sites_cart_selection[1] = False
assert bond_proxies.asu.size() == 0
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(),
bond_simple_proxies=bond_proxies.simple)
manager = geometry_restraints.manager.manager(
bond_params_table=bond_params_table,
angle_proxies=angle_proxies)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
traditional_convergence_test=traditional_convergence_test,
drop_convergence_test_max_drop_eps=1.e-20,
drop_convergence_test_iteration_coefficient=1,
max_iterations=1000),
sites_cart_selection=sites_cart_selection,
)
assert minimized.minimizer.iter() > 100
sites_cart_minimized_1 = sites_cart.deep_copy()
if (0 or verbose):
dump_pdb(
file_name="minimized_1.pdb", sites_cart=sites_cart_minimized_1)
bond_deltas = geometry_restraints.bond_deltas(
sites_cart=sites_cart_minimized_1,
proxies=bond_proxies.simple)
angle_deltas = geometry_restraints.angle_deltas(
sites_cart=sites_cart_minimized_1,
proxies=angle_proxies)
if (0 or verbose):
for proxy,delta in zip(bond_proxies.simple, bond_deltas):
print "bond:", proxy.i_seqs, delta
for proxy,delta in zip(angle_proxies, angle_deltas):
print "angle:", proxy.i_seqs, delta
assert is_below_limit(
value=flex.max(flex.abs(bond_deltas)), limit=0, eps=1.e-6)
assert is_below_limit(
value=flex.max(flex.abs(angle_deltas)), limit=0, eps=2.e-6)
sites_cart += matrix.col((1,1,0)) - matrix.col(sites_cart.min())
unit_cell_lengths = list( matrix.col(sites_cart.max())
+ matrix.col((1,-1.2,4)))
unit_cell_lengths[1] *= 2
unit_cell_lengths[2] *= 2
xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=unit_cell_lengths,
space_group_symbol="P112"))
for serial,site in zip(count(1), sites_cart):
xray_structure.add_scatterer(xray.scatterer(
label="C%02d"%serial,
site=xray_structure.unit_cell().fractionalize(site)))
if (0 or verbose):
xray_structure.show_summary().show_scatterers()
p1_structure = (xray_structure
.apply_shift((-.5,-.5,0))
.expand_to_p1()
.apply_shift((.5,.5,0)))
for shift in [(1,0,0), (0,1,0), (0,0,1)]:
p1_structure.add_scatterers(p1_structure.apply_shift(shift).scatterers())
if (0 or verbose):
open("p1_structure.pdb", "w").write(p1_structure.as_pdb_file())
nonbonded_cutoff = 6.5
asu_mappings = xray_structure.asu_mappings(
buffer_thickness=nonbonded_cutoff)
bond_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
geometry_restraints.add_pairs(bond_asu_table, bond_proxies.simple)
shell_asu_tables = crystal.coordination_sequences.shell_asu_tables(
pair_asu_table=bond_asu_table,
max_shell=3)
shell_sym_tables = [shell_asu_table.extract_pair_sym_table()
for shell_asu_table in shell_asu_tables]
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(),
bond_simple_proxies=bond_proxies.simple)
atom_energy_types = flex.std_string(sites_cart.size(), "Default")
nonbonded_params = geometry_restraints.nonbonded_params(
factor_1_4_interactions=vdw_1_4_factor,
const_shrink_1_4_interactions=0,
default_distance=default_vdw_distance)
nonbonded_params.distance_table.setdefault(
"Default")["Default"] = default_vdw_distance
pair_proxies = geometry_restraints.pair_proxies(
bond_params_table=bond_params_table,
shell_asu_tables=shell_asu_tables,
model_indices=None,
conformer_indices=None,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_distance_cutoff_plus_buffer=nonbonded_cutoff)
if (0 or verbose):
print "pair_proxies.bond_proxies.n_total():", \
pair_proxies.bond_proxies.n_total(),
print "simple:", pair_proxies.bond_proxies.simple.size(),
print "sym:", pair_proxies.bond_proxies.asu.size()
print "pair_proxies.nonbonded_proxies.n_total():", \
pair_proxies.nonbonded_proxies.n_total(),
print "simple:", pair_proxies.nonbonded_proxies.simple.size(),
print "sym:", pair_proxies.nonbonded_proxies.asu.size()
print "min_distance_nonbonded: %.2f" % flex.min(
geometry_restraints.nonbonded_deltas(
sites_cart=sites_cart,
sorted_asu_proxies=pair_proxies.nonbonded_proxies))
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart,
f=s,
prefix="[]")
assert s.getvalue().splitlines()[0] == "[]Histogram of bond lengths:"
assert s.getvalue().splitlines()[5].startswith("[] 1.80 - 1.80:")
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_deltas(
sites_cart=sites_cart,
f=s,
prefix="][")
assert s.getvalue().splitlines()[0] == "][Histogram of bond deltas:"
assert s.getvalue().splitlines()[5].startswith("][ 0.000 - 0.000:")
s = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
max_items=3,
f=s,
prefix=":;")
l = s.getvalue().splitlines()
assert l[0] == ":;Bond restraints: 18"
assert l[1] == ":;Sorted by residual:"
assert l[2].startswith(":;bond ")
assert l[3].startswith(":; ")
assert l[4] == ":; ideal model delta sigma weight residual"
for i in [5,-2]:
assert l[i].startswith(":; 1.800 1.800 ")
assert l[-1] == ":;... (remaining 15 not shown)"
s = StringIO()
pair_proxies.nonbonded_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart,
f=s,
prefix="]^")
assert not show_diff(s.getvalue(), """\
]^Histogram of nonbonded interaction distances:
]^ 2.16 - 3.03: 3
]^ 3.03 - 3.89: 12
]^ 3.89 - 4.75: 28
]^ 4.75 - 5.61: 44
]^ 5.61 - 6.48: 54
""")
s = StringIO()
pair_proxies.nonbonded_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
max_items=7,
f=s,
prefix=">,")
assert not show_diff(s.getvalue(), """\
>,Nonbonded interactions: 141
>,Sorted by model distance:
>,nonbonded 15
>, 15
>, model vdw sym.op.
>, 2.164 3.600 -x+2,-y+1,z
...
>,nonbonded 4
>, 8
>, model vdw
>, 3.414 3.600
>,... (remaining 134 not shown)
""",
selections=[range(6), range(-5,0)])
vdw_1_sticks = []
vdw_2_sticks = []
for proxy in pair_proxies.nonbonded_proxies.simple:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(pml_stick(
begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
else:
vdw_2_sticks.append(pml_stick(
begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
mps = asu_mappings.mappings()
for proxy in pair_proxies.nonbonded_proxies.asu:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(pml_stick(
begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
else:
vdw_2_sticks.append(pml_stick(
begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
if (0 or verbose):
pml_write(f=open("vdw_1.pml", "w"), label="vdw_1", sticks=vdw_1_sticks)
pml_write(f=open("vdw_2.pml", "w"), label="vdw_2", sticks=vdw_2_sticks)
#
i_pdb = count(2)
for use_crystal_symmetry in [False, True]:
if (not use_crystal_symmetry):
crystal_symmetry = None
site_symmetry_table = None
else:
crystal_symmetry = xray_structure
site_symmetry_table = xray_structure.site_symmetry_table()
for sites_cart in [sites_cart_manual.deep_copy(),
sites_cart_minimized_1.deep_copy()]:
manager = geometry_restraints.manager.manager(
crystal_symmetry=crystal_symmetry,
site_symmetry_table=site_symmetry_table,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_function=geometry_restraints.prolsq_repulsion_function(),
bond_params_table=bond_params_table,
shell_sym_tables=shell_sym_tables,
nonbonded_distance_cutoff=nonbonded_cutoff,
nonbonded_buffer=1,
angle_proxies=angle_proxies,
plain_pairs_radius=5)
manager = manager.select(selection=flex.bool(sites_cart.size(), True))
manager = manager.select(
iselection=flex.size_t_range(stop=sites_cart.size()))
pair_proxies = manager.pair_proxies(sites_cart=sites_cart)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=1000))
if (0 or verbose):
minimized.final_target_result.show()
print "number of function evaluations:", minimized.minimizer.nfun()
print "n_updates_pair_proxies:", manager.n_updates_pair_proxies
if (not use_crystal_symmetry):
assert minimized.final_target_result.bond_residual_sum < 1.e-3
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
else:
assert minimized.final_target_result.bond_residual_sum < 1.e-2
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
assert minimized.final_target_result.angle_residual_sum < 1.e-3
if (0 or verbose):
pdb_file_name = "minimized_%d.pdb" % i_pdb.next()
print "Writing file:", pdb_file_name
dump_pdb(file_name=pdb_file_name, sites_cart=sites_cart)
if (manager.site_symmetry_table is None):
additional_site_symmetry_table = None
else:
additional_site_symmetry_table = sgtbx.site_symmetry_table()
assert manager.new_including_isolated_sites(
n_additional_sites=0,
site_symmetry_table=additional_site_symmetry_table,
nonbonded_types=flex.std_string()).plain_pairs_radius \
== manager.plain_pairs_radius
if (crystal_symmetry is not None):
assert len(manager.plain_pair_sym_table) == 16
if (0 or verbose):
manager.plain_pair_sym_table.show()
#
xray_structure.set_u_iso(values=flex.double([
0.77599982480241358, 0.38745781137212021, 0.20667558236418682,
0.99759840171302094, 0.8917287406687805, 0.64780251325379845,
0.24878590382983534, 0.59480621182194615, 0.58695637792905142,
0.33997130213653637, 0.51258699130743735, 0.79760289141276675,
0.39996577657875021, 0.4329328819341467, 0.70422156561726479,
0.87260110626999332]))
class parameters: pass
parameters.sphere_radius = 5
parameters.distance_power = 0.7
parameters.average_power = 0.9
parameters.wilson_b_weight = 1.3952
parameters.wilson_b_weight_auto = False
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=None,
use_hd=False,
use_u_local_only = False,
compute_gradients=False,
gradients=None,
normalization=False,
collect=True)
assert adp_energies.number_of_restraints == 69
assert approx_equal(adp_energies.residual_sum, 6.24865382467)
assert adp_energies.gradients is None
assert adp_energies.u_i.size() == adp_energies.number_of_restraints
assert adp_energies.u_j.size() == adp_energies.number_of_restraints
assert adp_energies.r_ij.size() == adp_energies.number_of_restraints
for wilson_b in [None, 10, 100]:
finite_difference_gradients = flex.double()
eps = 1.e-6
for i_scatterer in xrange(xray_structure.scatterers().size()):
rs = []
for signed_eps in [eps, -eps]:
xray_structure_eps = xray_structure.deep_copy_scatterers()
xray_structure_eps.scatterers()[i_scatterer].u_iso += signed_eps
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure_eps,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only = False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
rs.append(adp_energies.residual_sum)
assert adp_energies.gradients.size() \
== xray_structure.scatterers().size()
assert adp_energies.u_i == None
assert adp_energies.u_j == None
assert adp_energies.r_ij == None
finite_difference_gradients.append((rs[0]-rs[1])/(2*eps))
sel = flex.bool(xray_structure.scatterers().size(), True)
xray_structure.scatterers().flags_set_grad_u_iso(sel.iselection())
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only = False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
assert approx_equal(adp_energies.gradients, finite_difference_gradients)
print "OK"
