Exemplo n.º 1
0
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
Exemplo n.º 2
0
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
Exemplo n.º 3
0
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
Exemplo n.º 6
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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
Exemplo n.º 7
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
Exemplo n.º 8
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 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
Exemplo n.º 9
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
Exemplo n.º 10
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