def exercise(args, distance_cutoff=3.5, max_shell=5):
command_line = (iotbx_option_parser()
.option(None, "--tag",
action="store",
type="string")
.option(None, "--full",
action="store_true")
.option(None, "--verbose",
action="store_true")
).process(args=args)
co = command_line.options
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(): input file not available"
return
all_entries = strudat.read_all_entries(open(atlas_file))
for i,entry in enumerate(all_entries.entries):
structure = entry.as_xray_structure()
if (co.tag is not None):
if (co.tag != entry.tag):
continue
elif (not (co.full or i % 20 == 0)):
continue
if (co.verbose):
print "strudat tag:", entry.tag
exercise_simple(
structure, distance_cutoff, max_shell, co.verbose)
exercise_shell_asu_tables(structure, co.verbose)
def process_zeolite_atlas(args):
command_line = (iotbx_option_parser().option(
None, "--tag", action="store",
type="string").option(None, "--verbose",
action="store_true")).process(args=args)
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 process_zeolite_atlas(): input file not available")
return
if (command_line.options.verbose):
out = sys.stdout
else:
out = StringIO()
with open(atlas_file) as f:
all_entries = strudat.read_all_entries(f)
for i, entry in enumerate(all_entries.entries):
structure = entry.as_xray_structure()
if (command_line.options.tag is not None):
if (command_line.options.tag != entry.tag):
continue
print("strudat tag:", entry.tag, file=out)
exercise(structure=structure, out=out)
exercise_shake_sites_in_place(structure=structure)
def get_emma_model_from_strudat(file_name):
strudat_entries = strudat.read_all_entries(open(file_name))
if (len(strudat_entries.entries) > 1):
raise MultipleEntriesError(
"strudat file %s may contain only one structure." % file_name)
assert len(strudat_entries.entries) == 1
return strudat_entries.entries[0].as_xray_structure().as_emma_model()
def process_zeolite_atlas(args):
command_line = (iotbx_option_parser()
.option(None, "--tag",
action="store",
type="string")
.option(None, "--verbose",
action="store_true")
).process(args=args)
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 process_zeolite_atlas(): input file not available"
return
if (command_line.options.verbose):
out = sys.stdout
else:
out = StringIO()
all_entries = strudat.read_all_entries(open(atlas_file))
for i,entry in enumerate(all_entries.entries):
structure = entry.as_xray_structure()
if (command_line.options.tag is not None):
if (command_line.options.tag != entry.tag):
continue
print >> out, "strudat tag:", entry.tag
exercise(structure=structure, out=out)
exercise_shake_sites_in_place(structure=structure)
def exercise_zeolite_atlas(distance_cutoff=3.5):
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_zeolite_atlas(): input file not available")
return
with open(atlas_file) as f:
all_entries = strudat.read_all_entries(f)
for i, entry in enumerate(all_entries.entries):
structure = entry.as_xray_structure()
if ("--full" in sys.argv[1:] or i % 20 == 0):
tst_direct_space_asu.exercise_neighbors_pair_generators(
structure=structure, verbose="--Verbose" in sys.argv[1:])
asu_mappings = structure.asu_mappings(buffer_thickness=distance_cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=distance_cutoff)
bond_counts = flex.size_t(structure.scatterers().size(), 0)
for pair in pair_generator:
bond_counts[pair.i_seq] += 1
if (pair.j_sym == 0):
bond_counts[pair.j_seq] += 1
for atom, bond_count in zip(entry.atoms, bond_counts):
assert atom.connectivity is not None
assert atom.connectivity == bond_count
def get_emma_model_from_strudat(file_name):
strudat_entries = strudat.read_all_entries(open(file_name))
if (len(strudat_entries.entries) > 1):
raise MultipleEntriesError(
"strudat file %s may contain only one structure." % file_name)
assert len(strudat_entries.entries) == 1
return strudat_entries.entries[0].as_xray_structure().as_emma_model()
def exercise_zeolite_atlas(distance_cutoff=3.5):
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_zeolite_atlas(): input file not available"
return
all_entries = strudat.read_all_entries(open(atlas_file))
for i,entry in enumerate(all_entries.entries):
structure = entry.as_xray_structure()
if ("--full" in sys.argv[1:] or i % 20 == 0):
tst_direct_space_asu.exercise_neighbors_pair_generators(
structure=structure,
verbose="--Verbose" in sys.argv[1:])
asu_mappings = structure.asu_mappings(buffer_thickness=distance_cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff)
bond_counts = flex.size_t(structure.scatterers().size(), 0)
for pair in pair_generator:
bond_counts[pair.i_seq] += 1
if (pair.j_sym == 0):
bond_counts[pair.j_seq] += 1
for atom,bond_count in zip(entry.atoms, bond_counts):
assert atom.connectivity is not None
assert atom.connectivity == bond_count
def exercise(args, distance_cutoff=3.5, max_shell=5):
command_line = (iotbx_option_parser().option(
None, "--tag", action="store",
type="string").option(None, "--full", action="store_true").option(
None, "--verbose", action="store_true")).process(args=args)
co = command_line.options
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(): input file not available"
return
all_entries = strudat.read_all_entries(open(atlas_file))
for i, entry in enumerate(all_entries.entries):
structure = entry.as_xray_structure()
if (co.tag is not None):
if (co.tag != entry.tag):
continue
elif (not (co.full or i % 20 == 0)):
continue
if (co.verbose):
print "strudat tag:", entry.tag
exercise_simple(structure, distance_cutoff, max_shell, co.verbose)
exercise_shell_asu_tables(structure, co.verbose)
def exercise_all():
verbose = "--verbose" in sys.argv[1:]
exercise_icosahedron(verbose=verbose)
default_distance_cutoff = 3.5
regression_misc = libtbx.env.find_in_repositories("phenix_regression/misc")
if (regression_misc is None):
print "Skipping exercise_all(): phenix_regression/misc not available"
return
def get_reference_dict(file_name):
path = os.path.join(regression_misc, file_name)
if (not os.path.isfile(path)):
print "Skipping some tests: reference file not available:", path
return None
result = {}
for line in open(path).read().splitlines():
tag, data = line.split()
assert not tag in result
result[tag] = data
return result
reference_apatanl_dict = get_reference_dict(
"angle_pair_asu_tables_as_nested_lists")
reference_cppc_dict = get_reference_dict(
"conservative_pair_proxies_counts")
file_names = []
for file_name in ["strudat_zeolite_atlas", "strudat_special_bonds"]:
path = os.path.join(regression_misc, file_name)
if (not os.path.isfile(path)):
print "Skipping %s test: input file not available" % file_name
else:
file_names.append(path)
for file_name in file_names:
strudat_entries = strudat.read_all_entries(open(file_name))
for i_entry,entry in enumerate(strudat_entries.entries):
if ( file_name.endswith("strudat_zeolite_atlas")
and not ("--full" in sys.argv[1:] or i_entry % 20 == 0)):
continue
if (0 or verbose):
print "strudat tag:", entry.tag
structure = entry.as_xray_structure()
if (0 or verbose):
structure.show_summary().show_scatterers()
if (entry.title.startswith("cutoff")):
distance_cutoff = float(entry.title.split()[1])
else:
distance_cutoff = default_distance_cutoff
weak_check_sym_equiv = (
entry.reference.find("weak_check_sym_equiv") >= 0)
connectivities = entry.connectivities(all_or_nothing=True)
if (1):
exercise(
structure=structure,
distance_cutoff=distance_cutoff,
connectivities=connectivities,
weak_check_sym_equiv=weak_check_sym_equiv,
verbose=verbose)
if (0 or verbose):
print
if (file_name.endswith("strudat_zeolite_atlas")):
exercise_bond_sorted_asu_proxies(
structure=structure,
distance_cutoff=distance_cutoff)
if (reference_apatanl_dict is None):
reference_apatanl = None
else:
assert entry.tag in reference_apatanl_dict
reference_apatanl = reference_apatanl_dict[entry.tag]
if (reference_cppc_dict is None):
reference_cppc = None
else:
assert entry.tag in reference_cppc_dict
reference_cppc = reference_cppc_dict[entry.tag]
exercise_angle_pair_asu_table(
structure=structure,
distance_cutoff=distance_cutoff,
connectivities=connectivities,
reference_apatanl=reference_apatanl,
reference_cppc=reference_cppc)
def run(args, distance_cutoff=3.5):
from iotbx.option_parser import option_parser
command_line = (option_parser(
usage="iotbx.distance_least_squares [options] studat_file [...]",
description="Example: iotbx.distance_least_squares strudat --tag=SOD"
).option(
None,
"--tag",
action="store",
type="string",
help="tag as it appears in the strudat file").option(
None,
"--repulsion_function",
action="store",
type="choice",
choices=["gaussian", "cos", "prolsq"],
default="gaussian",
help="Nonbonded repulsion function type",
metavar="gaussian|cos|prolsq").option(
None,
"--bond_stretch_factor",
action="store",
type="float",
default=0.1,
help="Bond stretch factor used in max residual calculation"
" for nonbonded cos or gaussian repulsion function",
metavar="FLOAT").option(
None,
"--n_trials",
action="store",
type="int",
default=1,
help="Number of trial per structure",
metavar="INT").option(
None,
"--n_macro_cycles",
action="store",
type="int",
default=1,
help="Number of macro cycles per trial",
metavar="INT").option(
None, "--dev", action="store_true",
default=False)).process(args=args)
if (len(command_line.args) == 0):
command_line.parser.show_help()
return
co = command_line.options
from cctbx.geometry_restraints import distance_least_squares as dls
from iotbx.kriber import strudat
for file_name in command_line.args:
strudat_entries = strudat.read_all_entries(open(file_name))
for entry in strudat_entries.entries:
if (co.tag is not None and co.tag != entry.tag):
continue
print("strudat tag:", entry.tag)
print()
dls.distance_and_repulsion_least_squares(
si_structure=entry.as_xray_structure(),
distance_cutoff=distance_cutoff,
nonbonded_repulsion_function_type=co.repulsion_function,
nonbonded_max_residual_bond_stretch_factor=co.
bond_stretch_factor,
n_trials=co.n_trials,
n_macro_cycles=co.n_macro_cycles,
connectivities=entry.connectivities(all_or_nothing=True),
dev=co.dev)
def run(args):
command_line = (option_parser(
usage="iotbx.show_distances [options] studat_file [...]",
description="Example: iotbx.show_distances strudat --tag=SOD")
.option(None, "--cif_data_block_name",
action="store",
type="string",
default=None,
help="data block name as it appears in the CIF file")
.option(None, "--tag",
action="store",
type="string",
help="tag as it appears in the strudat file")
.option(None, "--distance_cutoff",
action="store",
type="float",
default=5,
help="Maximum distance to be considered",
metavar="FLOAT")
.option(None, "--min_distance_sym_equiv",
action="store",
type="float",
default=0.5,
help="Minimum distance between symmetry mates"
" (for special position analysis)",
metavar="FLOAT")
.option(None, "--show_cartesian",
action="store_true",
help="Show Cartesian coordinates (instead of fractional)")
.enable_symmetry_comprehensive()
.option(None, "--cs",
action="store",
type="int",
help="Compute N terms of the coordination sequences",
metavar="N")
.option(None, "--coseq",
action="store",
type="string",
help="name of file with known coordination sequences",
metavar="FILE")
).process(args=args)
if (len(command_line.args) == 0):
command_line.parser.show_help()
return
co = command_line.options
max_shell = co.cs
if (co.coseq is not None):
coseq_dict = coordination_sequences.get_kriber_coseq_file(
file_name=co.coseq)
if (max_shell is None): max_shell = 10
else:
coseq_dict = None
def call_display(xray_structure):
display(
distance_cutoff=co.distance_cutoff,
show_cartesian=co.show_cartesian,
max_shell=max_shell,
coseq_dict=coseq_dict,
xray_structure=xray_structure)
cif_data_block_name_use_counter = 0
for file_name in command_line.args:
xray_structure = None
if (iotbx.pdb.is_pdb_file(file_name=file_name)):
xray_structure = iotbx.pdb.input(
file_name=file_name).xray_structure_simple(
crystal_symmetry=command_line.symmetry,
cryst1_substitution_buffer_layer=max(5,
co.distance_cutoff+1),
min_distance_sym_equiv=co.min_distance_sym_equiv,
enable_scattering_type_unknown=True)
call_display(xray_structure)
continue
if (file_name.lower().endswith(".cif")):
xray_structures = iotbx.cif.reader(
file_path=file_name).build_crystal_structures()
if (co.cif_data_block_name is not None):
xray_structure = xray_structures.get(co.cif_data_block_name)
if (xray_structure is None):
continue
cif_data_block_name_use_counter += 1
xray_structures = [xray_structure]
else:
xray_structures = xray_structures.values()
for xray_structure in xray_structures:
call_display(xray_structure)
continue
if ( file_name.endswith(".ins")
or file_name.endswith(".res")):
xray_structure = xray.structure.from_shelx(
filename=file_name, strictly_shelxl=False)
call_display(xray_structure)
continue
if (command_line.symmetry is not None
and (command_line.symmetry.unit_cell() is not None
or command_line.symmetry.space_group_info() is not None)):
raise Sorry(
"Command-line symmetry options not supported for strudat files.")
strudat_entries = strudat.read_all_entries(open(file_name))
for entry in strudat_entries.entries:
if ( co.tag is not None
and co.tag != entry.tag):
continue
print "strudat tag:", entry.tag
print
xray_structure = entry.as_xray_structure(
min_distance_sym_equiv=co.min_distance_sym_equiv)
call_display(xray_structure)
if ( co.cif_data_block_name is not None
and cif_data_block_name_use_counter == 0):
raise Sorry(
"cif_data_block_name %s not found in any input files"
% show_string(co.cif_data_block_name))
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
""")
def exercise_basic():
test_file = StringIO("""
*tric
Title
Reference
P 1
11 12 13 100 110 120
Si 0.1 0.2 0.3
---------------------------------
*mono_b
Title
Reference
P 1 2 1
11 12 13 100
Si 0.1 0.2 0.3
---------------------------------
*mono_c
Title
Reference
P 1 1 2
11 12 13 100
Si 0.1 0.2 0.3
---------------------------------
*mono_a
Title
Reference
P 2 1 1
11 12 13 100
Si 0.1 0.2 0.3
---------------------------------
*orth
Title
Reference
P 2 2 2
11 12 13
Si 0.1 0.2 0.3 # remark
---------------------------------
*tetr
Title
Reference
P 4
11 13
Si 0.1 0.2 0.3 4
---------------------------------
*trig
Title
Reference
R 3
11 13
Si 0.1 0.2 0.3
---------------------------------
*rhom
Title
Reference
R 3 R
11 100
Si 0.1 0.2 0.3
---------------------------------
*hexa
Title
Reference
P 6
11 13
Si 0.1 0.2 0.3
---------------------------------
*cubi
Title
Reference
P 2 3
11
Si 0.1 0.2 0.3
O 0.0 0.0 0.0
---------------------------------
*mixcon1
Title
Reference
P 2 3
11
Si 0.1 0.2 0.3 4
O 0.0 0.0 0.0
---------------------------------
*mixcon2
Title
Reference
P 2 3
11
Si 0.1 0.2 0.3 4
O 0.0 0.0 0.0
O 0.0 0.0 0.0
---------------------------------
""")
all_entries = strudat.read_all_entries(test_file)
for tag, cell in (("tric", (11, 12, 13, 100, 110,
120)), ("mono_b", (11, 12, 13, 90, 100, 90)),
("mono_c", (11, 12, 13, 90, 90,
100)), ("mono_a", (11, 12, 13, 100, 90, 90)),
("orth", (11, 12, 13, 90, 90,
90)), ("tetr", (11, 11, 13, 90, 90, 90)),
("trig", (11, 11, 13, 90, 90,
120)), ("rhom", (11, 11, 11, 100, 100, 100)),
("hexa", (11, 11, 13, 90, 90,
120)), ("cubi", (11, 11, 11, 90, 90, 90))):
assert all_entries.get(tag).unit_cell().is_similar_to(
uctbx.unit_cell(cell))
assert all_entries.get("orth").atoms[0].connectivity is None
assert all_entries.get("tetr").atoms[0].connectivity == 4
assert all_entries.get("mixcon1").connectivities() == [4, None]
assert all_entries.get("mixcon2").connectivities() == [4, None, None]
try:
all_entries.get("mixcon1").connectivities(all_or_nothing=True)
except AssertionError as e:
assert str(e) == "Tag mixcon1: 1 atom is missing the bond count."
else:
raise Exception_expected
try:
all_entries.get("mixcon2").connectivities(all_or_nothing=True)
except AssertionError as e:
assert str(e) == "Tag mixcon2: 2 atoms are missing the bond count."
else:
raise Exception_expected
assert all_entries.get("cubi").as_xray_structure().scatterers().size() == 2
def exercise_basic():
test_file = StringIO("""
*tric
Title
Reference
P 1
11 12 13 100 110 120
Si 0.1 0.2 0.3
---------------------------------
*mono_b
Title
Reference
P 1 2 1
11 12 13 100
Si 0.1 0.2 0.3
---------------------------------
*mono_c
Title
Reference
P 1 1 2
11 12 13 100
Si 0.1 0.2 0.3
---------------------------------
*mono_a
Title
Reference
P 2 1 1
11 12 13 100
Si 0.1 0.2 0.3
---------------------------------
*orth
Title
Reference
P 2 2 2
11 12 13
Si 0.1 0.2 0.3 # remark
---------------------------------
*tetr
Title
Reference
P 4
11 13
Si 0.1 0.2 0.3 4
---------------------------------
*trig
Title
Reference
R 3
11 13
Si 0.1 0.2 0.3
---------------------------------
*rhom
Title
Reference
R 3 R
11 100
Si 0.1 0.2 0.3
---------------------------------
*hexa
Title
Reference
P 6
11 13
Si 0.1 0.2 0.3
---------------------------------
*cubi
Title
Reference
P 2 3
11
Si 0.1 0.2 0.3
O 0.0 0.0 0.0
---------------------------------
*mixcon1
Title
Reference
P 2 3
11
Si 0.1 0.2 0.3 4
O 0.0 0.0 0.0
---------------------------------
*mixcon2
Title
Reference
P 2 3
11
Si 0.1 0.2 0.3 4
O 0.0 0.0 0.0
O 0.0 0.0 0.0
---------------------------------
""")
all_entries = strudat.read_all_entries(test_file)
for tag,cell in (("tric", (11,12,13,100,110,120)),
("mono_b", (11,12,13,90,100,90)),
("mono_c", (11,12,13,90,90,100)),
("mono_a", (11,12,13,100,90,90)),
("orth", (11,12,13,90,90,90)),
("tetr", (11,11,13,90,90,90)),
("trig", (11,11,13,90,90,120)),
("rhom", (11,11,11,100,100,100)),
("hexa", (11,11,13,90,90,120)),
("cubi", (11,11,11,90,90,90))):
assert all_entries.get(tag).unit_cell().is_similar_to(
uctbx.unit_cell(cell))
assert all_entries.get("orth").atoms[0].connectivity is None
assert all_entries.get("tetr").atoms[0].connectivity == 4
assert all_entries.get("mixcon1").connectivities() == [4, None]
assert all_entries.get("mixcon2").connectivities() == [4, None, None]
try:
all_entries.get("mixcon1").connectivities(all_or_nothing=True)
except AssertionError, e:
assert str(e) == "Tag mixcon1: 1 atom is missing the bond count."
def run_call_back(flags,
space_group_info,
max_n_indices=5,
anomalous_flag=True):
if (not flags.Verbose):
out = StringIO()
else:
out = sys.stdout
if (flags.chunk):
chunk_n,chunk_i = [int(i) for i in flags.chunk.split(",")]
else:
chunk_n = 1
chunk_i = 0
if (flags.tag):
if (flags.tag == "internal"):
strudat_contents = strudat.read_all_entries(StringIO(zeolite_edi))
strudat_entries = strudat_contents.entries
else:
atlas_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/strudat_zeolite_atlas",
test=os.path.isfile)
assert atlas_file is not None
strudat_contents = strudat.read_all_entries(open(atlas_file))
if (not isinstance(flags.tag, str)):
strudat_entries = strudat_contents.entries
else:
strudat_entries = [strudat_contents.get(tag=flags.tag)]
assert strudat_entries[0] is not None
if (flags.isotropic):
use_u_aniso_flags = [False]
elif (flags.anisotropic):
use_u_aniso_flags = [True]
else:
use_u_aniso_flags = [False, True]
if (not flags.tag):
for n_scatterers in xrange(2,3+1):
for use_u_aniso in use_u_aniso_flags:
xray_structure = random_structure.xray_structure(
space_group_info=space_group_info,
n_scatterers=n_scatterers,
elements="random",
volume_per_atom=100,
general_positions_only=False,
random_f_prime_d_min=1,
random_f_double_prime=anomalous_flag,
use_u_aniso = use_u_aniso,
use_u_iso = not(use_u_aniso),
random_u_iso=True,
random_u_iso_scale=0.3,
random_occupancy=True)
exercise(
xray_structure=xray_structure,
anomalous_flag=anomalous_flag,
max_n_indices=max_n_indices,
out=out)
out.flush()
else:
i_structure = count()
for entry in strudat_entries:
if (i_structure.next() % chunk_n != chunk_i): continue
print >> sys.stderr, "strudat tag:", entry.tag
sys.stderr.flush()
print >> out, "strudat tag:", entry.tag
out.flush()
for use_u_aniso in use_u_aniso_flags:
xray_structure = entry.as_xray_structure()
xray_structure = random_structure.xray_structure(
space_group_info=xray_structure.space_group_info(),
unit_cell=xray_structure.unit_cell(),
sites_frac=xray_structure.sites_frac(),
elements="random",
random_f_prime_d_min=1,
random_f_double_prime=anomalous_flag,
use_u_aniso = use_u_aniso,
use_u_iso = not(use_u_aniso),
random_u_iso=True,
random_u_iso_scale=0.3,
random_occupancy=True)
exercise(
xray_structure=xray_structure,
anomalous_flag=anomalous_flag,
max_n_indices=max_n_indices,
out=out)
out.flush()
if (flags.tag):
return False
def run(args):
command_line = (option_parser(
usage="iotbx.python strudat_as_fis.py [options] studat_file [...]")
.option(None, "--tag",
action="store",
type="string",
help="tag as it appears in the strudat file")
.option(None, "--coseq",
action="store",
type="string",
help="name of file with known coordination sequences",
metavar="FILE")
).process(args=args)
if (len(command_line.args) == 0):
command_line.parser.show_help()
return
if (command_line.options.coseq is not None):
coseq_dict = coordination_sequences.get_kriber_coseq_file(
file_name=command_line.options.coseq)
else:
coseq_dict = None
n_fis = 0
n_errors = 0
for file_name in command_line.args:
strudat_entries = strudat.read_all_entries(open(file_name))
for entry in strudat_entries.entries:
if ( command_line.options.tag is not None
and command_line.options.tag != entry.tag):
continue
print "strudat tag:", entry.tag
print
xray_structure = entry.as_xray_structure()
pairs, term_table = display(
distance_cutoff=3.4,
show_cartesian=False,
max_shell=10,
coseq_dict=coseq_dict,
xray_structure=xray_structure)
fis = format_focus_input(
tag=entry.tag,
xray_structure=xray_structure,
term_table=term_table)
open("tmp.fis", "w").write(fis)
open("%s.fis" % entry.tag, "w").write(fis)
n_fis += 1
if (os.path.isfile("tmp.fo")):
os.remove("tmp.fo")
assert not os.path.isfile("tmp.fo")
focus_run = easy_run.fully_buffered(
command="focus -siteframe -sitelabel -coseq=10 tmp.fis > tmp.fo")
focus_run.raise_if_errors_or_output()
lines = open("tmp.fo").read().splitlines()
focus_coseq = extract_coseq(lines=lines)
for scatterer,terms in zip(xray_structure.scatterers(), term_table):
focus_terms = focus_coseq[scatterer.label]
if (list(terms) != focus_terms):
print "ERROR:", entry.tag
print " cctbx", list(terms)
print " focus", focus_terms
n_errors += 1
print "Number of .fis files written:", n_fis
print "Number of errors:", n_errors
for file_name in ["tmp.fis", "tmp.fo"]:
if (os.path.isfile(file_name)):
os.remove(file_name)
def run(args):
command_line = (option_parser(
usage="iotbx.show_distances [options] studat_file [...]",
description="Example: iotbx.show_distances strudat --tag=SOD").option(
None,
"--cif_data_block_name",
action="store",
type="string",
default=None,
help="data block name as it appears in the CIF file").option(
None,
"--tag",
action="store",
type="string",
help="tag as it appears in the strudat file").option(
None,
"--distance_cutoff",
action="store",
type="float",
default=5,
help="Maximum distance to be considered",
metavar="FLOAT"
).option(
None,
"--min_distance_sym_equiv",
action="store",
type="float",
default=0.5,
help="Minimum distance between symmetry mates"
" (for special position analysis)",
metavar="FLOAT"
).option(
None,
"--show_cartesian",
action="store_true",
help="Show Cartesian coordinates (instead of fractional)"
).enable_symmetry_comprehensive().option(
None,
"--cs",
action="store",
type="int",
help="Compute N terms of the coordination sequences",
metavar="N").option(
None,
"--coseq",
action="store",
type="string",
help="name of file with known coordination sequences",
metavar="FILE")).process(args=args)
if (len(command_line.args) == 0):
command_line.parser.show_help()
return
co = command_line.options
max_shell = co.cs
if (co.coseq is not None):
coseq_dict = coordination_sequences.get_kriber_coseq_file(
file_name=co.coseq)
if (max_shell is None): max_shell = 10
else:
coseq_dict = None
def call_display(xray_structure):
display(distance_cutoff=co.distance_cutoff,
show_cartesian=co.show_cartesian,
max_shell=max_shell,
coseq_dict=coseq_dict,
xray_structure=xray_structure)
cif_data_block_name_use_counter = 0
for file_name in command_line.args:
xray_structure = None
if (iotbx.pdb.is_pdb_file(file_name=file_name)):
xray_structure = iotbx.pdb.input(
file_name=file_name).xray_structure_simple(
crystal_symmetry=command_line.symmetry,
cryst1_substitution_buffer_layer=max(
5, co.distance_cutoff + 1),
min_distance_sym_equiv=co.min_distance_sym_equiv,
enable_scattering_type_unknown=True)
call_display(xray_structure)
continue
if (file_name.lower().endswith(".cif")):
xray_structures = iotbx.cif.reader(
file_path=file_name).build_crystal_structures()
if (co.cif_data_block_name is not None):
xray_structure = xray_structures.get(co.cif_data_block_name)
if (xray_structure is None):
continue
cif_data_block_name_use_counter += 1
xray_structures = [xray_structure]
else:
xray_structures = xray_structures.values()
for xray_structure in xray_structures:
call_display(xray_structure)
continue
if (file_name.endswith(".ins") or file_name.endswith(".res")):
xray_structure = xray.structure.from_shelx(filename=file_name,
strictly_shelxl=False)
call_display(xray_structure)
continue
if (command_line.symmetry is not None
and (command_line.symmetry.unit_cell() is not None
or command_line.symmetry.space_group_info() is not None)):
raise Sorry(
"Command-line symmetry options not supported for strudat files."
)
strudat_entries = strudat.read_all_entries(open(file_name))
for entry in strudat_entries.entries:
if (co.tag is not None and co.tag != entry.tag):
continue
print "strudat tag:", entry.tag
print
xray_structure = entry.as_xray_structure(
min_distance_sym_equiv=co.min_distance_sym_equiv)
call_display(xray_structure)
if (co.cif_data_block_name is not None
and cif_data_block_name_use_counter == 0):
raise Sorry("cif_data_block_name %s not found in any input files" %
show_string(co.cif_data_block_name))
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_all():
verbose = "--verbose" in sys.argv[1:]
exercise_icosahedron(verbose=verbose)
default_distance_cutoff = 3.5
regression_misc = libtbx.env.find_in_repositories("phenix_regression/misc")
if (regression_misc is None):
print("Skipping exercise_all(): phenix_regression/misc not available")
return
def get_reference_dict(file_name):
path = os.path.join(regression_misc, file_name)
if (not os.path.isfile(path)):
print("Skipping some tests: reference file not available:", path)
return None
result = {}
for line in open(path).read().splitlines():
tag, data = line.split()
assert not tag in result
result[tag] = data
return result
reference_apatanl_dict = get_reference_dict(
"angle_pair_asu_tables_as_nested_lists")
reference_cppc_dict = get_reference_dict(
"conservative_pair_proxies_counts")
file_names = []
for file_name in ["strudat_zeolite_atlas", "strudat_special_bonds"]:
path = os.path.join(regression_misc, file_name)
if (not os.path.isfile(path)):
print("Skipping %s test: input file not available" % file_name)
else:
file_names.append(path)
for file_name in file_names:
strudat_entries = strudat.read_all_entries(open(file_name))
for i_entry, entry in enumerate(strudat_entries.entries):
if (file_name.endswith("strudat_zeolite_atlas")
and not ("--full" in sys.argv[1:] or i_entry % 20 == 0)):
continue
if (0 or verbose):
print("strudat tag:", entry.tag)
structure = entry.as_xray_structure()
if (0 or verbose):
structure.show_summary().show_scatterers()
if (entry.title.startswith("cutoff")):
distance_cutoff = float(entry.title.split()[1])
else:
distance_cutoff = default_distance_cutoff
weak_check_sym_equiv = (
entry.reference.find("weak_check_sym_equiv") >= 0)
connectivities = entry.connectivities(all_or_nothing=True)
if (1):
exercise(structure=structure,
distance_cutoff=distance_cutoff,
connectivities=connectivities,
weak_check_sym_equiv=weak_check_sym_equiv,
verbose=verbose)
if (0 or verbose):
print()
if (file_name.endswith("strudat_zeolite_atlas")):
exercise_bond_sorted_asu_proxies(
structure=structure, distance_cutoff=distance_cutoff)
if (reference_apatanl_dict is None):
reference_apatanl = None
else:
assert entry.tag in reference_apatanl_dict
reference_apatanl = reference_apatanl_dict[entry.tag]
if (reference_cppc_dict is None):
reference_cppc = None
else:
assert entry.tag in reference_cppc_dict
reference_cppc = reference_cppc_dict[entry.tag]
exercise_angle_pair_asu_table(structure=structure,
distance_cutoff=distance_cutoff,
connectivities=connectivities,
reference_apatanl=reference_apatanl,
reference_cppc=reference_cppc)
def run(args, distance_cutoff=3.5):
from iotbx.option_parser import option_parser
command_line = (option_parser(
usage="iotbx.distance_least_squares [options] studat_file [...]",
description="Example: iotbx.distance_least_squares strudat --tag=SOD")
.option(None, "--tag",
action="store",
type="string",
help="tag as it appears in the strudat file")
.option(None, "--repulsion_function",
action="store",
type="choice",
choices=["gaussian", "cos", "prolsq"],
default="gaussian",
help="Nonbonded repulsion function type",
metavar="gaussian|cos|prolsq")
.option(None, "--bond_stretch_factor",
action="store",
type="float",
default=0.1,
help="Bond stretch factor used in max residual calculation"
" for nonbonded cos or gaussian repulsion function",
metavar="FLOAT")
.option(None, "--n_trials",
action="store",
type="int",
default=1,
help="Number of trial per structure",
metavar="INT")
.option(None, "--n_macro_cycles",
action="store",
type="int",
default=1,
help="Number of macro cycles per trial",
metavar="INT")
.option(None, "--dev",
action="store_true",
default=False)
).process(args=args)
if (len(command_line.args) == 0):
command_line.parser.show_help()
return
co = command_line.options
from cctbx.geometry_restraints import distance_least_squares as dls
from iotbx.kriber import strudat
for file_name in command_line.args:
strudat_entries = strudat.read_all_entries(open(file_name))
for entry in strudat_entries.entries:
if (co.tag is not None and co.tag != entry.tag):
continue
print "strudat tag:", entry.tag
print
dls.distance_and_repulsion_least_squares(
si_structure=entry.as_xray_structure(),
distance_cutoff=distance_cutoff,
nonbonded_repulsion_function_type=co.repulsion_function,
nonbonded_max_residual_bond_stretch_factor=co.bond_stretch_factor,
n_trials=co.n_trials,
n_macro_cycles=co.n_macro_cycles,
connectivities=entry.connectivities(all_or_nothing=True),
dev=co.dev)