def _nonbonded_pair_objects(
max_bonded_cutoff=3.,
i_seqs=None,
):
if i_seqs is None:
atoms = self.pdb_hierarchy.atoms()
i_seqs = flex.size_t()
for atom in atoms:
i_seqs.append(atom.i_seq)
if (self.model_indices is not None):
model_indices = self.model_indices.select(i_seqs)
conformer_indices = self.conformer_indices.select(i_seqs)
sym_excl_indices = self.sym_excl_indices.select(i_seqs)
donor_acceptor_excl_groups = self.donor_acceptor_excl_groups.select(
i_seqs)
asu_mappings = self.special_position_settings.asu_mappings(
buffer_thickness=max_bonded_cutoff)
sites_cart = self.sites_cart.select(i_seqs)
asu_mappings.process_sites_cart(
original_sites=sites_cart,
site_symmetry_table=self.site_symmetry_table().select(i_seqs))
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
nonbonded_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
model_indices=model_indices,
conformer_indices=conformer_indices,
sym_excl_indices=sym_excl_indices,
donor_acceptor_excl_groups=donor_acceptor_excl_groups,
nonbonded_params=geometry_restraints.nonbonded_params(
default_distance=1),
nonbonded_types=flex.std_string(conformer_indices.size()),
nonbonded_charges=flex.int(conformer_indices.size(), 0),
nonbonded_distance_cutoff_plus_buffer=max_bonded_cutoff,
min_cubicle_edge=5,
shell_asu_tables=[pair_asu_table])
return nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, i_seqs
def _nonbonded_pair_objects(max_bonded_cutoff=3.,
i_seqs=None,
):
if i_seqs is None:
atoms = self.pdb_hierarchy.atoms()
i_seqs = flex.size_t()
for atom in atoms:
i_seqs.append(atom.i_seq)
if (self.model_indices is not None):
model_indices = self.model_indices.select(i_seqs)
conformer_indices = self.conformer_indices.select(i_seqs)
sym_excl_indices = self.sym_excl_indices.select(i_seqs)
donor_acceptor_excl_groups = self.donor_acceptor_excl_groups.select(i_seqs)
asu_mappings = self.special_position_settings.asu_mappings(
buffer_thickness=max_bonded_cutoff)
sites_cart = self.sites_cart.select(i_seqs)
asu_mappings.process_sites_cart(
original_sites=sites_cart,
site_symmetry_table=self.site_symmetry_table().select(i_seqs))
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
nonbonded_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
model_indices=model_indices,
conformer_indices=conformer_indices,
sym_excl_indices=sym_excl_indices,
donor_acceptor_excl_groups=donor_acceptor_excl_groups,
nonbonded_params=geometry_restraints.nonbonded_params(
default_distance=1),
nonbonded_types=flex.std_string(conformer_indices.size()),
nonbonded_charges=flex.int(conformer_indices.size(), 0),
nonbonded_distance_cutoff_plus_buffer=max_bonded_cutoff,
min_cubicle_edge=5,
shell_asu_tables=[pair_asu_table])
return nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, i_seqs
def exercise_with_zeolite(verbose):
if (not libtbx.env.has_module("iotbx")):
print("Skipping exercise_with_zeolite(): iotbx not available")
return
from iotbx.kriber import strudat
atlas_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/strudat_zeolite_atlas",
test=os.path.isfile)
if (atlas_file is None):
print("Skipping exercise_with_zeolite(): input file not available")
return
strudat_contents = strudat.read_all_entries(open(atlas_file))
strudat_entry = strudat_contents.get("YUG")
si_structure = strudat_entry.as_xray_structure()
if (verbose):
out = sys.stdout
else:
out = StringIO()
drls = distance_and_repulsion_least_squares(
si_structure=si_structure,
distance_cutoff=3.5,
nonbonded_repulsion_function_type="prolsq",
n_macro_cycles=2,
out=out)
#
nbp = drls.geometry_restraints_manager.pair_proxies().nonbonded_proxies
assert nbp.n_total() > 50
# expected is 60, but the exact number depends on the minimizer
#
site_labels = drls.minimized_structure.scatterers().extract_labels()
sites_cart = drls.start_structure.sites_cart()
pair_proxies = drls.geometry_restraints_manager.pair_proxies()
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out)
if (verbose):
sys.stdout.write(out.getvalue())
assert len(out.getvalue().splitlines()) == 48 * 4 + 2
assert out.getvalue().splitlines()[-1].find("remaining") < 0
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="0^",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"),
"""\
0^Bond restraints: 48
0^Sorted by residual:
0^bond O3
0^ O4
0^ ideal model delta sigma weight residual
0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
0^bond SI1
0^ SI1
0^ ideal model delta sigma weight residual sym.op.
0^ 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
0^... (remaining 20 not shown)
""",
selections=[range(6), range(-5, 0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="0^",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"),
"""\
0^Bond restraints: 48
0^Sorted by delta:
0^bond O3
0^ O4
0^ ideal model delta sigma weight residual
0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
0^... (remaining 20 not shown)
""",
selections=[range(6), [-1]])
site_labels_long = ["abc" + label + "def" for label in site_labels]
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels_long,
f=out,
prefix="^0",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"),
"""\
^0Bond restraints: 48
^0Sorted by residual:
^0bond abcO3def
^0 abcO4def
^0 ideal model delta sigma weight residual
^0 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
^0bond abcSI1def
^0 abcSI1def
^0 ideal model delta sigma weight residual sym.op.
^0 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
^0... (remaining 20 not shown)
""",
selections=[range(6), range(-5, 0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
f=out,
prefix=".=",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"),
"""\
.=Bond restraints: 48
.=Sorted by residual:
.=bond 4
.= 5
.= ideal model delta sigma weight residual
.= 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
.=bond 0
.= 0
.= ideal model delta sigma weight residual sym.op.
.= 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
.=... (remaining 20 not shown)
""",
selections=[range(6), range(-5, 0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
f=out,
prefix="-+",
max_items=1)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(
out.getvalue().replace("e-00", "e-0"), """\
-+Bond restraints: 48
-+Sorted by residual:
-+bond 4
-+ 5
-+ ideal model delta sigma weight residual
-+ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
-+... (remaining 47 not shown)
""")
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
f=out,
prefix="=+",
max_items=0)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(
out.getvalue(), """\
=+Bond restraints: 48
=+Sorted by residual:
=+... (remaining 48 not shown)
""")
#
sites_cart = si_structure.sites_cart()
site_labels = [sc.label for sc in si_structure.scatterers()]
asu_mappings = si_structure.asu_mappings(buffer_thickness=3.5)
for min_cubicle_edge in [0, 5]:
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=asu_mappings.buffer_thickness(),
minimal=False,
min_cubicle_edge=min_cubicle_edge)
sorted_asu_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
asu_mappings=asu_mappings)
while (not pair_generator.at_end()):
p = geometry_restraints.nonbonded_asu_proxy(
pair=next(pair_generator), vdw_distance=3)
sorted_asu_proxies.process(p)
out = StringIO()
sorted_asu_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="d%")
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(
out.getvalue(),
"""\
d%Nonbonded interactions: 7
d%Sorted by model distance:
...
d%nonbonded SI2
d% SI2
d% model vdw sym.op.
d% 3.092 3.000 -x+1,y,-z
...
d%nonbonded SI1
d% SI1
d% model vdw sym.op.
d% 3.216 3.000 -x+1/2,-y+1/2,-z+1
""",
selections=[range(2), range(10, 14),
range(26, 30)])
out = StringIO()
sorted_asu_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
f=out,
prefix="*j",
max_items=5)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(),
"""\
*jNonbonded interactions: 7
*jSorted by model distance:
...
*jnonbonded 0
*j 1
*j model vdw
*j 3.107 3.000
*jnonbonded 0
*j 0
*j model vdw sym.op.
*j 3.130 3.000 -x+1,y,-z+1
*j... (remaining 2 not shown)
""",
selections=[range(2), range(-9, 0)])
out = StringIO()
sorted_asu_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
f=out,
prefix="@r",
max_items=0)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
@rNonbonded interactions: 7
""")
def exercise_with_zeolite(verbose):
if (not libtbx.env.has_module("iotbx")):
print "Skipping exercise_with_zeolite(): iotbx not available"
return
from iotbx.kriber import strudat
atlas_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/strudat_zeolite_atlas",
test=os.path.isfile)
if (atlas_file is None):
print "Skipping exercise_with_zeolite(): input file not available"
return
strudat_contents = strudat.read_all_entries(open(atlas_file))
strudat_entry = strudat_contents.get("YUG")
si_structure = strudat_entry.as_xray_structure()
if (verbose):
out = sys.stdout
else:
out = StringIO()
drls = distance_and_repulsion_least_squares(
si_structure=si_structure,
distance_cutoff=3.5,
nonbonded_repulsion_function_type="prolsq",
n_macro_cycles=2,
out=out)
#
nbp = drls.geometry_restraints_manager.pair_proxies().nonbonded_proxies
assert nbp.n_total() > 50
# expected is 60, but the exact number depends on the minimizer
#
site_labels = drls.minimized_structure.scatterers().extract_labels()
sites_cart = drls.start_structure.sites_cart()
pair_proxies = drls.geometry_restraints_manager.pair_proxies()
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out)
if (verbose):
sys.stdout.write(out.getvalue())
assert len(out.getvalue().splitlines()) == 48*4+2
assert out.getvalue().splitlines()[-1].find("remaining") < 0
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="0^",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
0^Bond restraints: 48
0^Sorted by residual:
0^bond O3
0^ O4
0^ ideal model delta sigma weight residual
0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
0^bond SI1
0^ SI1
0^ ideal model delta sigma weight residual sym.op.
0^ 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
0^... (remaining 20 not shown)
""",
selections=[range(6), range(-5,0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="0^",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
0^Bond restraints: 48
0^Sorted by delta:
0^bond O3
0^ O4
0^ ideal model delta sigma weight residual
0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
0^... (remaining 20 not shown)
""",
selections=[range(6), [-1]])
site_labels_long = ["abc"+label+"def" for label in site_labels]
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels_long,
f=out,
prefix="^0",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
^0Bond restraints: 48
^0Sorted by residual:
^0bond abcO3def
^0 abcO4def
^0 ideal model delta sigma weight residual
^0 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
^0bond abcSI1def
^0 abcSI1def
^0 ideal model delta sigma weight residual sym.op.
^0 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
^0... (remaining 20 not shown)
""",
selections=[range(6), range(-5,0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
f=out,
prefix=".=",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
.=Bond restraints: 48
.=Sorted by residual:
.=bond 4
.= 5
.= ideal model delta sigma weight residual
.= 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
.=bond 0
.= 0
.= ideal model delta sigma weight residual sym.op.
.= 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
.=... (remaining 20 not shown)
""",
selections=[range(6), range(-5,0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
f=out,
prefix="-+",
max_items=1)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
-+Bond restraints: 48
-+Sorted by residual:
-+bond 4
-+ 5
-+ ideal model delta sigma weight residual
-+ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
-+... (remaining 47 not shown)
""")
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
f=out,
prefix="=+",
max_items=0)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
=+Bond restraints: 48
=+Sorted by residual:
=+... (remaining 48 not shown)
""")
#
sites_cart = si_structure.sites_cart()
site_labels = [sc.label for sc in si_structure.scatterers()]
asu_mappings = si_structure.asu_mappings(buffer_thickness=3.5)
for min_cubicle_edge in [0, 5]:
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=asu_mappings.buffer_thickness(),
minimal=False,
min_cubicle_edge=min_cubicle_edge)
sorted_asu_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
asu_mappings=asu_mappings)
while (not pair_generator.at_end()):
p = geometry_restraints.nonbonded_asu_proxy(
pair=pair_generator.next(),
vdw_distance=3)
sorted_asu_proxies.process(p)
out = StringIO()
sorted_asu_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="d%")
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
d%Nonbonded interactions: 7
d%Sorted by model distance:
...
d%nonbonded SI2
d% SI2
d% model vdw sym.op.
d% 3.092 3.000 -x+1,y,-z
...
d%nonbonded SI1
d% SI1
d% model vdw sym.op.
d% 3.216 3.000 -x+1/2,-y+1/2,-z+1
""",
selections=[range(2), range(10,14), range(26,30)])
out = StringIO()
sorted_asu_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
f=out,
prefix="*j",
max_items=5)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
*jNonbonded interactions: 7
*jSorted by model distance:
...
*jnonbonded 0
*j 1
*j model vdw
*j 3.107 3.000
*jnonbonded 0
*j 0
*j model vdw sym.op.
*j 3.130 3.000 -x+1,y,-z+1
*j... (remaining 2 not shown)
""",
selections=[range(2), range(-9,0)])
out = StringIO()
sorted_asu_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
f=out,
prefix="@r",
max_items=0)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
@rNonbonded interactions: 7
""")
