def exercise_sdb(verbose=0):
structure = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("P 31"),
elements=["N", "C", "C", "O"] * 2,
volume_per_atom=500,
min_distance=2.,
general_positions_only=False,
random_u_iso=True)
f_abs = abs(
structure.structure_factors(anomalous_flag=False,
d_min=2,
algorithm="direct").f_calc())
sdb_out = structure.as_cns_sdb_file(file="foo.sdb",
description="random_structure",
comment=["any", "thing"],
group="best")
if (0 or verbose):
sys.stdout.write(sdb_out)
sdb_files = sdb_reader.multi_sdb_parser(StringIO(sdb_out))
assert len(sdb_files) == 1
structure_read = sdb_files[0].as_xray_structure(
crystal_symmetry=crystal.symmetry(unit_cell=structure.unit_cell(),
space_group_info=None))
f_read = abs(
f_abs.structure_factors_from_scatterers(xray_structure=structure_read,
algorithm="direct").f_calc())
regression = flex.linear_regression(f_abs.data(), f_read.data())
assert regression.is_well_defined()
if (0 or verbose):
regression.show_summary()
assert abs(regression.slope() - 1) < 1.e-4
assert abs(regression.y_intercept()) < 1.e-3
def exercise_sdb(verbose=0):
structure = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("P 31"),
elements=["N","C","C","O"]*2,
volume_per_atom=500,
min_distance=2.,
general_positions_only=False,
random_u_iso=True)
f_abs = abs(structure.structure_factors(
anomalous_flag=False, d_min=2, algorithm="direct").f_calc())
sdb_out = structure.as_cns_sdb_file(
file="foo.sdb",
description="random_structure",
comment=["any", "thing"],
group="best")
if (0 or verbose):
sys.stdout.write(sdb_out)
sdb_files = sdb_reader.multi_sdb_parser(StringIO(sdb_out))
assert len(sdb_files) == 1
structure_read = sdb_files[0].as_xray_structure(
crystal_symmetry=crystal.symmetry(
unit_cell=structure.unit_cell(),
space_group_info=None))
f_read = abs(f_abs.structure_factors_from_scatterers(
xray_structure=structure_read, algorithm="direct").f_calc())
regression = flex.linear_regression(f_abs.data(), f_read.data())
assert regression.is_well_defined()
if (0 or verbose):
regression.show_summary()
assert abs(regression.slope()-1) < 1.e-4
assert abs(regression.y_intercept()) < 1.e-3
def sdb_files_as_xray_structures(lines, unit_cell, space_group_info, min_distance_sym_equiv):
sdb_files = sdb_reader.multi_sdb_parser(lines)
xray_structures = []
for sdb in sdb_files:
if (unit_cell is not None): sdb.unit_cell = unit_cell
if (space_group_info is not None): sdb.space_group_info = space_group_info
xray_structure = sdb.as_xray_structure(min_distance_sym_equiv=min_distance_sym_equiv)
xray_structures.append(xray_structure)
return xray_structures
def extract_from(file_name=None, file=None):
assert [file_name, file].count(None) == 1
if (file is None):
file = open(file_name)
sdb_files = sdb_reader.multi_sdb_parser(file)
assert len(sdb_files) > 0
crystal_symmetry = sdb_files[0].crystal_symmetry()
assert [crystal_symmetry.unit_cell(),
crystal_symmetry.space_group_info()].count(None) < 2
return crystal_symmetry
def extract_from(file_name=None, file=None):
assert [file_name, file].count(None) == 1
if (file is None):
file = open(file_name)
sdb_files = sdb_reader.multi_sdb_parser(file)
assert len(sdb_files) > 0
crystal_symmetry = sdb_files[0].crystal_symmetry()
assert [crystal_symmetry.unit_cell(),
crystal_symmetry.space_group_info()].count(None) < 2
return crystal_symmetry
def sdb_files_as_xray_structures(lines, unit_cell, space_group_info,
min_distance_sym_equiv):
sdb_files = sdb_reader.multi_sdb_parser(lines)
xray_structures = []
for sdb in sdb_files:
if (unit_cell is not None): sdb.unit_cell = unit_cell
if (space_group_info is not None):
sdb.space_group_info = space_group_info
xray_structure = sdb.as_xray_structure(
min_distance_sym_equiv=min_distance_sym_equiv)
xray_structures.append(xray_structure)
return xray_structures
def __init__(self,
ucparams,
sgsymbol,
convention,
format,
coor_type,
skip_columns,
coordinates,
other_symmetry=None):
self.ucparams = ucparams
self.sgsymbol = sgsymbol
self.convention = convention
self.other_symmetry = other_symmetry
self.coordinate_format = None
if (format == "generic"):
skip_columns = io_utils.interpret_skip_columns(skip_columns)
self.positions = []
for line in coordinates:
label, site = interpret_generic_coordinate_line(
line, skip_columns)
if (label == ""): label = "Site" + str(len(self.positions) + 1)
if (coor_type != "Fractional"):
site = self.get_unit_cell().fractionalize(site)
self.positions.append(emma.position(label, site))
self.coordinate_format = "generic"
else:
if (self.coordinate_format is None):
try:
import iotbx.pdb
pdb_inp = iotbx.pdb.input(source_info=None,
lines=coordinates)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
self.pdb_model = pdb_file_to_emma_model(
self.crystal_symmetry(), pdb_inp, other_symmetry)
if (len(self.pdb_model.positions()) > 0):
self.coordinate_format = "pdb"
if (self.coordinate_format is None):
try:
from iotbx.cns import sdb_reader
self.sdb_files = sdb_reader.multi_sdb_parser(coordinates)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
self.coordinate_format = "sdb"
if (self.coordinate_format is None):
raise RuntimeError("Coordinate format unknown.")
self.i_next_model = 0
def __init__(self, ucparams, sgsymbol, convention,
format, coor_type, skip_columns, coordinates,
other_symmetry=None):
self.ucparams = ucparams
self.sgsymbol = sgsymbol
self.convention = convention
self.other_symmetry = other_symmetry
self.coordinate_format = None
if (format == "generic"):
skip_columns = io_utils.interpret_skip_columns(skip_columns)
self.positions = []
for line in coordinates:
label, site = interpret_generic_coordinate_line(line, skip_columns)
if (label == ""): label = "Site" + str(len(self.positions)+1)
if (coor_type != "Fractional"):
site = self.get_unit_cell().fractionalize(site)
self.positions.append(emma.position(label, site))
self.coordinate_format = "generic"
else:
if (self.coordinate_format is None):
try:
import iotbx.pdb
pdb_inp = iotbx.pdb.input(source_info=None, lines=coordinates)
except KeyboardInterrupt: raise
except Exception:
pass
else:
self.pdb_model = pdb_file_to_emma_model(
self.crystal_symmetry(), pdb_inp, other_symmetry)
if (len(self.pdb_model.positions()) > 0):
self.coordinate_format = "pdb"
if (self.coordinate_format is None):
try:
from iotbx.cns import sdb_reader
self.sdb_files = sdb_reader.multi_sdb_parser(coordinates)
except KeyboardInterrupt: raise
except Exception:
pass
else:
self.coordinate_format = "sdb"
if (self.coordinate_format is None):
raise RuntimeError("Coordinate format unknown.")
self.i_next_model = 0
def get_emma_model_from_sdb(file_name, crystal_symmetry):
sdb_files = sdb_reader.multi_sdb_parser(open(file_name))
if (len(sdb_files) > 1):
raise MultipleEntriesError(
"SDB file %s may contain only one structure." % file_name)
assert len(sdb_files) == 1
sdb_file = sdb_files[0]
crystal_symmetry = crystal_symmetry.join_symmetry(
other_symmetry=sdb_file.crystal_symmetry(),
force=True)
positions = []
for i,site in enumerate(sdb_file.sites):
if (crystal_symmetry.unit_cell() is None):
raise RuntimeError("Unit cell parameters unknown.")
positions.append(emma.position(
":".join((str(i+1), site.segid, site.type)),
crystal_symmetry.unit_cell().fractionalize((site.x, site.y, site.z))))
assert len(positions) > 0
result = emma.model(
crystal_symmetry.special_position_settings(),
positions)
result.label = sdb_file.file_name
return result
def get_emma_model_from_sdb(file_name, crystal_symmetry):
sdb_files = sdb_reader.multi_sdb_parser(open(file_name))
if (len(sdb_files) > 1):
raise MultipleEntriesError(
"SDB file %s may contain only one structure." % file_name)
assert len(sdb_files) == 1
sdb_file = sdb_files[0]
crystal_symmetry = crystal_symmetry.join_symmetry(
other_symmetry=sdb_file.crystal_symmetry(), force=True)
positions = []
for i, site in enumerate(sdb_file.sites):
if (crystal_symmetry.unit_cell() is None):
raise RuntimeError("Unit cell parameters unknown.")
positions.append(
emma.position(
":".join((str(i + 1), site.segid, site.type)),
crystal_symmetry.unit_cell().fractionalize(
(site.x, site.y, site.z))))
assert len(positions) > 0
result = emma.model(crystal_symmetry.special_position_settings(),
positions)
result.label = sdb_file.file_name
return result