def exercise_validation():
cd = validation.smart_load_dictionary(name="cif_core.dic")
assert isinstance(cd.deepcopy(), validation.dictionary)
assert cd.deepcopy() == cd
assert isinstance(cd.copy(), validation.dictionary)
assert cd.copy() == cd
#
cm_invalid = cif.reader(input_string=cif_invalid).model()
s = StringIO()
cm_invalid.validate(cd, out=s)
assert sorted(cd.err.errors.keys()) == [
2001, 2002, 2101, 2102, 2501, 2503, 2504, 2505, 2506]
assert sorted(cd.err.warnings.keys()) == [1001, 1002, 1003]
cm_valid = cif.reader(input_string=cif_valid).model()
cd.err.reset()
s = StringIO()
cm_valid.validate(cd, out=s)
assert len(cd.err.errors.keys()) == 0
assert len(cd.err.warnings.keys()) == 0
cd2 = validation.smart_load_dictionary(name="cif_mm.dic")
cm_invalid_2 = cif.reader(input_string=cif_invalid_2).model()
s = StringIO()
cm_invalid_2.validate(cd2, out=s)
assert sorted(cd2.err.errors.keys()) == [
2001, 2101, 2102, 2201, 2202, 2203, 2301, 2503, 2504]
assert cd2.err.error_count == 12
assert sorted(cd2.err.warnings.keys()) == [1001, 1002]
def exercise_validation():
cd = validation.smart_load_dictionary(name="cif_core.dic")
assert isinstance(cd.deepcopy(), validation.dictionary)
assert cd.deepcopy() == cd
assert isinstance(cd.copy(), validation.dictionary)
assert cd.copy() == cd
#
cm_invalid = cif.reader(input_string=cif_invalid).model()
s = StringIO()
cm_invalid.validate(cd, out=s)
assert sorted(cd.err.errors.keys()) == [
2001, 2002, 2101, 2102, 2501, 2503, 2504, 2505, 2506
]
assert sorted(cd.err.warnings.keys()) == [1001, 1002, 1003]
cm_valid = cif.reader(input_string=cif_valid).model()
cd.err.reset()
s = StringIO()
cm_valid.validate(cd, out=s)
assert len(list(cd.err.errors.keys())) == 0
assert len(list(cd.err.warnings.keys())) == 0
cd2 = validation.smart_load_dictionary(name="cif_mm.dic")
cm_invalid_2 = cif.reader(input_string=cif_invalid_2).model()
s = StringIO()
cm_invalid_2.validate(cd2, out=s)
assert sorted(cd2.err.errors.keys()) == [
2001, 2101, 2102, 2201, 2202, 2203, 2301, 2503, 2504
]
assert cd2.err.error_count == 12
assert sorted(cd2.err.warnings.keys()) == [1001, 1002]
def run(args, out=sys.stdout):
if len(args) == 0: args = ["--help"]
command_line = (option_parser(
usage="iotbx.cif.validate filepath|directory [options]").option(
None, "--file_ext", action="store", default="cif").option(
None, "--dic", action="append", dest="dictionaries").option(
None, "--show_warnings", action="store_true").option(
None, "--show_timings", action="store_true").option(
None,
"--strict",
action="store",
type="bool",
default="true")).process(args=args)
if len(command_line.args) != 1:
command_line.parser.show_help()
return
total_timer = time_log("total").start()
filepath = command_line.args[0]
if not os.path.isabs(filepath):
abs_path = libtbx.env.find_in_repositories(relative_path=filepath)
if abs_path is None:
abs_path = libtbx.env.find_in_repositories(relative_path=filepath,
test=os.path.isfile)
if abs_path is not None: filepath = abs_path
cif_dics = command_line.options.dictionaries
if cif_dics is None:
cif_dics = ["cif_core.dic"]
cif_dic = validation.smart_load_dictionary(name=cif_dics[0])
if len(cif_dics) > 1:
[
cif_dic.update(validation.smart_load_dictionary(name=d))
for d in cif_dics[1:]
]
show_warnings = command_line.options.show_warnings == True
show_timings = command_line.options.show_timings == True
strict = command_line.options.strict
if os.path.isdir(filepath):
file_ext = command_line.options.file_ext
crawl(filepath,
file_ext=file_ext,
cif_dic=cif_dic,
show_warnings=show_warnings,
show_timings=show_timings,
strict=strict)
elif os.path.isfile(filepath):
cm = cif.reader(file_path=filepath, strict=strict).model()
cm.validate(cif_dic, show_warnings=show_warnings)
else:
try:
file_object = urllib.request.urlopen(filepath)
except urllib.error.URLError as e:
pass
else:
cm = cif.reader(file_object=file_object, strict=strict).model()
cm.validate(cif_dic, show_warnings=show_warnings)
if show_timings:
total_timer.stop()
print(total_timer.report())
def run(args, out=sys.stdout):
if len(args) == 0: args = ["--help"]
command_line = (option_parser(
usage="iotbx.cif.validate filepath|directory [options]")
.option(None, "--file_ext",
action="store",
default="cif")
.option(None, "--dic",
action="append",
dest="dictionaries")
.option(None, "--show_warnings",
action="store_true")
.option(None, "--show_timings",
action="store_true")
.option(None, "--strict",
action="store",
type="bool",
default="true")).process(args=args)
if len(command_line.args) != 1:
command_line.parser.show_help()
return
total_timer = time_log("total").start()
filepath = command_line.args[0]
if not os.path.isabs(filepath):
abs_path = libtbx.env.find_in_repositories(relative_path=filepath)
if abs_path is None:
abs_path = libtbx.env.find_in_repositories(
relative_path=filepath, test=os.path.isfile)
if abs_path is not None: filepath = abs_path
cif_dics = command_line.options.dictionaries
if cif_dics is None:
cif_dics = ["cif_core.dic"]
cif_dic = validation.smart_load_dictionary(name=cif_dics[0])
if len(cif_dics) > 1:
[cif_dic.update(
validation.smart_load_dictionary(name=d)) for d in cif_dics[1:]]
show_warnings = command_line.options.show_warnings == True
show_timings = command_line.options.show_timings == True
strict = command_line.options.strict
if os.path.isdir(filepath):
file_ext = command_line.options.file_ext
crawl(filepath, file_ext=file_ext,
cif_dic=cif_dic, show_warnings=show_warnings,
show_timings=show_timings, strict=strict)
elif os.path.isfile(filepath):
cm = cif.reader(file_path=filepath, strict=strict).model()
cm.validate(cif_dic, show_warnings=show_warnings)
else:
try:
file_object = urllib2.urlopen(filepath)
except urllib2.URLError, e:
pass
else:
def run_implementation(server_info, inp, status):
cif_text = inp.cif_text
if cif_text is None:
cif_text = inp.cif_file
reader = iotbx.cif.reader(input_string=cif_text, raise_if_errors=False)
if reader.error_count():
print "Errors encountered during parsing"
return
else:
print "No parsing errors."
if inp.cif_dic is not None:
cif_dic = validation.smart_load_dictionary(name=inp.cif_dic)
print
print "Validating CIF against %s:" % inp.cif_dic
cif_model = reader.model()
error_handler = cif_model.validate(cif_dic, show_warnings=True)
if len(error_handler.warnings) + len(error_handler.errors) == 0:
print "No validation errors found."
print
if inp.extract_miller_arrays:
print "Extracting Miller arrays:"
try:
miller_arrays = reader.as_miller_arrays()
except iotbx.cif.builders.CifBuilderError, e:
print "CifBuilderError: %s" % str(e)
else:
for ma in miller_arrays:
print ma
ma.show_comprehensive_summary()
if len(miller_arrays) == 0:
print "No Miller arrays found."
print
def run_implementation(server_info, inp, status):
cif_text = inp.cif_text
if cif_text is None:
cif_text = inp.cif_file
reader = iotbx.cif.reader(input_string=cif_text, raise_if_errors=False)
if reader.error_count():
print("Errors encountered during parsing")
return
else:
print("No parsing errors.")
if inp.cif_dic is not None:
cif_dic = validation.smart_load_dictionary(name=inp.cif_dic)
print()
print("Validating CIF against %s:" % inp.cif_dic)
cif_model = reader.model()
error_handler = cif_model.validate(cif_dic, show_warnings=True)
if len(error_handler.warnings) + len(error_handler.errors) == 0:
print("No validation errors found.")
print()
if inp.extract_miller_arrays:
print("Extracting Miller arrays:")
try:
miller_arrays = reader.as_miller_arrays()
except iotbx.cif.builders.CifBuilderError as e:
print("CifBuilderError: %s" % str(e))
else:
for ma in miller_arrays:
print(ma)
ma.show_comprehensive_summary()
if len(miller_arrays) == 0:
print("No Miller arrays found.")
print()
if inp.extract_crystal_structures:
print("Extracting crystal structures:")
try:
crystal_structures = reader.build_crystal_structures()
except iotbx.cif.builders.CifBuilderError as e:
print("CifBuilderError: %s" % str(e))
else:
for xs in crystal_structures.values():
xs.show_summary().show_scatterers()
print()
if len(crystal_structures) == 0:
print("No crystal structures found.")
print()
if inp.extract_pdb_hierarchy:
print("Extracting pdb.hierarchy:")
# TODO am I a dictionary ?- if so change me accordingly..
hierarchy = iotbx.pdb.mmcif.pdb_hierarchy_builder(
cif_model.blocks.values()[0]).hierarchy
hierarchy.show()
print()
def exercise_smart_load(show_timings=False, exercise_url=False):
from libtbx.test_utils import open_tmp_directory
from libtbx.utils import time_log
import libtbx
import os, shutil
name = ["cif_core.dic", "cif_mm.dic"][0]
url = [cif_core_dic_url, cif_mm_dic_url][0]
# from gz
gz_timer = time_log("from gz").start()
cd = validation.smart_load_dictionary(name=name)
gz_timer.stop()
if exercise_url:
tempdir = open_tmp_directory()
store_dir = libtbx.env.under_dist(module_name='iotbx',
path='cif/dictionaries')
file_path = os.path.join(store_dir, name) + '.gz'
shutil.copy(os.path.join(store_dir, name) + '.gz', tempdir)
# from url
url_timer = time_log("from url").start()
cd = validation.smart_load_dictionary(url=url, store_dir=tempdir)
url_timer.stop()
# from url to file
url_to_file_timer = time_log("url to file").start()
cd = validation.smart_load_dictionary(url=url,
save_local=True,
store_dir=tempdir)
url_to_file_timer.stop()
# read local file
file_timer = time_log("from file").start()
cd = validation.smart_load_dictionary(
file_path=os.path.join(tempdir, name))
file_timer.stop()
if show_timings:
print(time_log.legend)
print(gz_timer.report())
if exercise_url:
print(url_timer.report())
print(url_to_file_timer.report())
print(file_timer.report())
def exercise_smart_load(show_timings=False, exercise_url=False):
from libtbx.test_utils import open_tmp_directory
from libtbx.utils import time_log
import libtbx
import os, shutil
name = ["cif_core.dic", "cif_mm.dic"][0]
url = [cif_core_dic_url, cif_mm_dic_url][0]
# from gz
gz_timer = time_log("from gz").start()
cd = validation.smart_load_dictionary(name=name)
gz_timer.stop()
if exercise_url:
tempdir = open_tmp_directory()
store_dir = libtbx.env.under_dist(
module_name='iotbx', path='cif/dictionaries')
file_path = os.path.join(store_dir, name) + '.gz'
shutil.copy(os.path.join(store_dir, name) + '.gz', tempdir)
# from url
url_timer = time_log("from url").start()
cd = validation.smart_load_dictionary(url=url, store_dir=tempdir)
url_timer.stop()
# from url to file
url_to_file_timer = time_log("url to file").start()
cd = validation.smart_load_dictionary(
url=url, save_local=True, store_dir=tempdir)
url_to_file_timer.stop()
# read local file
file_timer = time_log("from file").start()
cd = validation.smart_load_dictionary(file_path=os.path.join(tempdir, name))
file_timer.stop()
if show_timings:
print time_log.legend
print gz_timer.report()
if exercise_url:
print url_timer.report()
print url_to_file_timer.report()
print file_timer.report()
def run_implementation(server_info, inp, status):
cif_text = inp.cif_text
if cif_text is None:
cif_text = inp.cif_file
reader = iotbx.cif.reader(input_string=cif_text, raise_if_errors=False)
if reader.error_count():
print "Errors encountered during parsing:"
errors = reader.parser.lexer_errors()
errors.extend(reader.parser.parser_errors())
for i, error in enumerate(errors):
print error
if i > 50: break
return
else:
print "No parsing errors."
if inp.cif_dic is not None:
cif_dic = validation.smart_load_dictionary(name=inp.cif_dic)
print
print "Validating CIF against %s:" %inp.cif_dic
cif_model = reader.model()
error_handler = cif_model.validate(cif_dic, show_warnings=True)
if len(error_handler.warnings) + len(error_handler.errors) == 0:
print "No validation errors found."
print
if inp.extract_miller_arrays:
print "Extracting Miller arrays:"
try:
miller_arrays = reader.as_miller_arrays()
except iotbx.cif.builders.CifBuilderError, e:
print "CifBuilderError: %s" %str(e)
else:
for ma in miller_arrays:
print ma
ma.show_comprehensive_summary()
if len(miller_arrays) == 0:
print "No Miller arrays found."
print
def run():
inp = iotbx.pdb.input(source_info=None, lines=quartz_as_cif.split('\n'))
modelm = mmtbx.model.manager(model_input=inp)
quartz_structure = modelm.get_xray_structure()
# Examine the site symmetry of each scatterer
for scatterer in quartz_structure.scatterers():
print "%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site
site_symmetry = quartz_structure.site_symmetry(scatterer.site)
print " point group type:", site_symmetry.point_group_type()
print " special position operator:", site_symmetry.special_op_simplified(
)
# Let's use scattering factors from the International Tables
modelm.setup_scattering_dictionaries(scattering_table="it1992")
quartz_structure = modelm.get_xray_structure()
# Now calculate some structure factors
f_calc = quartz_structure.structure_factors(d_min=2).f_calc()
f_calc_sq = f_calc.as_intensity_array()
f_calc_sq.show_summary().show_array()
# Output the intensities to a CIF file
# This probably should be deprecated as well
f_calc_sq.as_cif_simple(array_type="calc",
data_name="quartz",
out=open("quartz-intensities.cif", "wb"))
# Create an instance of model.cif, equivalent to a full CIF file
cif = model.cif()
# Create an instance of model.block, equivalent to a CIF data block
cif_block = model.block()
# Add the unit cell parameters to the cif_block
unit_cell = quartz_structure.unit_cell()
params = unit_cell.parameters()
cif_block["_cell_length_a"] = params[0]
cif_block["_cell_length_b"] = params[1]
cif_block["_cell_length_c"] = params[2]
cif_block["_cell_angle_alpha"] = params[3]
cif_block["_cell_angle_beta"] = params[4]
cif_block["_cell_angle_gamma"] = params[5]
cif_block["_cell_volume"] = unit_cell.volume()
# now we will create a CIF loop containing the space group symmetry operations
space_group = quartz_structure.space_group()
symop_loop = model.loop(header=("_space_group_symop_id",
"_space_group_symop_operation_xyz"))
for symop_id, symop in enumerate(space_group):
symop_loop.add_row((symop_id + 1, symop.as_xyz()))
# add the symop_loop and space group items to the cif_block
space_group_type = quartz_structure.space_group_info().type()
cif_block["_space_group_crystal_system"] = space_group.crystal_system(
).lower()
cif_block["_space_group_IT_number"] = space_group_type.number()
cif_block["_space_group_name_H-M_alt"] = space_group_type.lookup_symbol()
cif_block["_space_group_name_Hall"] = space_group_type.hall_symbol()
cif_block.add_loop(symop_loop)
# add cif_block to the cif object with the data block name "quartz"
cif["quartz"] = cif_block
# print the cif object to standard output
print cif
cif_model = iotbx.cif.reader(input_string=quartz_as_cif).model()
cif_model["quartz"]["_diffrn_radiation_probe"] = "xray"
cif_model["quartz"]["_space_group_crystal_system"] = "Monoclinic"
cif_model["quartz"]["_space_group_IT_number"] = "one hundred and eighty"
symop_loop.add_column("_space_group_symop_sg_id", [1] * 12)
cif_model["quartz"].add_loop(symop_loop)
pdbx_v50 = validation.smart_load_dictionary(name="mmcif_pdbx_v50.dic")
print "validation"
cif_model.validate(pdbx_v50, show_warnings=True)
def run():
quartz_as_cif = """\
data_quartz
_space_group_name_H-M_alt 'P 62 2 2'
_cell_length_a 5.01
_cell_length_b 5.01
_cell_length_c 5.47
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 120
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
Si Si 0.500 0.500 0.333 0.200
O O 0.197 -0.197 0.833 0.200
"""
import iotbx.cif
quartz_structure = iotbx.cif.reader(
input_string=quartz_as_cif).build_crystal_structures()["quartz"]
quartz_structure.show_summary().show_scatterers()
print
# Examine the site symmetry of each scatterer
for scatterer in quartz_structure.scatterers():
print "%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site
site_symmetry = quartz_structure.site_symmetry(scatterer.site)
print " point group type:", site_symmetry.point_group_type()
print " special position operator:", site_symmetry.special_op_simplified()
# Let's use scattering factors from the International Tables
quartz_structure.scattering_type_registry(table="it1992")
# Now calculate some structure factors
f_calc = quartz_structure.structure_factors(d_min=2).f_calc()
f_calc_sq = f_calc.as_intensity_array()
f_calc_sq.show_summary().show_array()
# Output the intensities to a CIF file
f_calc_sq.as_cif_simple(
array_type="calc", data_name="quartz", out=open("quartz.hkl", "wb"))
from iotbx.cif import model
# Create an instance of model.cif, equivalent to a full CIF file
cif = model.cif()
# Create an instance of model.block, equivalent to a CIF data block
cif_block = model.block()
# Add the unit cell parameters to the cif_block
unit_cell = quartz_structure.unit_cell()
params = unit_cell.parameters()
cif_block["_cell_length_a"] = params[0]
cif_block["_cell_length_b"] = params[1]
cif_block["_cell_length_c"] = params[2]
cif_block["_cell_angle_alpha"] = params[3]
cif_block["_cell_angle_beta"] = params[4]
cif_block["_cell_angle_gamma"] = params[5]
cif_block["_cell_volume"] = unit_cell.volume()
# now we will create a CIF loop containing the space group symmetry operations
space_group = quartz_structure.space_group()
symop_loop = model.loop(header=("_space_group_symop_id",
"_space_group_symop_operation_xyz"))
for symop_id, symop in enumerate(space_group):
symop_loop.add_row((symop_id + 1, symop.as_xyz()))
# add the symop_loop and space group items to the cif_block
space_group_type = quartz_structure.space_group_info().type()
cif_block["_space_group_crystal_system"] = space_group.crystal_system().lower()
cif_block["_space_group_IT_number"] = space_group_type.number()
cif_block["_space_group_name_H-M_alt"] = space_group_type.lookup_symbol()
cif_block["_space_group_name_Hall"] = space_group_type.hall_symbol()
cif_block.add_loop(symop_loop)
# add cif_block to the cif object with the data block name "quartz"
cif["quartz"] = cif_block
# print the cif object to standard output
print cif
from iotbx.cif import validation
cif_model = iotbx.cif.reader(input_string=quartz_as_cif).model()
cif_model["quartz"]["_diffrn_radiation_probe"] = "xray"
cif_model["quartz"]["_space_group_crystal_system"] = "Monoclinic"
cif_model["quartz"]["_space_group_IT_number"] = "one hundred and eighty"
symop_loop.add_column("_space_group_symop_sg_id", [1]*12)
cif_model["quartz"].add_loop(symop_loop)
cif_core_dic = validation.smart_load_dictionary(name="cif_core.dic")
cif_model.validate(cif_core_dic, show_warnings=True)