def run(args):
    assert len(args) > 0
    import iotbx.poscar
    for file_name in args:
        print(file_name)
        poscar = iotbx.poscar.reader(lines=open(file_name).read().splitlines(),
                                     source_info=file_name)
        poscar.make_up_types_if_necessary()
        poscar.xray_structure(u_iso=0.05).show_summary().show_scatterers()
        print()
def run(args):
  assert len(args) > 0
  import iotbx.poscar
  for file_name in args:
    print file_name
    poscar = iotbx.poscar.reader(
      lines=open(file_name).read().splitlines(),
      source_info=file_name)
    poscar.make_up_types_if_necessary()
    poscar.xray_structure(u_iso=0.05).show_summary().show_scatterers()
    print
Esempio n. 3
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def exercise():
    import libtbx.load_env
    import os
    op = os.path
    inp_dir = libtbx.env.find_in_repositories(
        relative_path="phenix_regression/poscar", test=op.isdir)
    if (inp_dir is None):
        print("Skipping POSCAR tests: input files not available")
        return
    import iotbx.poscar
    for node in os.listdir(inp_dir):
        if (not node.startswith("POSCAR-")): continue
        file_name = op.join(inp_dir, node)
        poscar = iotbx.poscar.reader(lines=open(file_name).read().splitlines())
        assert poscar.make_up_types_if_necessary() is poscar
        xs = poscar.xray_structure(u_iso=0.1)
        assert str(xs.space_group_info()) == "P 1"
        assert xs.scatterers().size() == len(poscar.sites)
Esempio n. 4
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def exercise():
  import libtbx.load_env
  import os
  op = os.path
  inp_dir = libtbx.env.find_in_repositories(
    relative_path="phenix_regression/poscar",
    test=op.isdir)
  if (inp_dir is None):
    print "Skipping POSCAR tests: input files not available"
    return
  import iotbx.poscar
  for node in os.listdir(inp_dir):
    if (not node.startswith("POSCAR-")): continue
    file_name = op.join(inp_dir, node)
    poscar = iotbx.poscar.reader(lines=open(file_name).read().splitlines())
    assert poscar.make_up_types_if_necessary() is poscar
    xs = poscar.xray_structure(u_iso=0.1)
    assert str(xs.space_group_info()) == "P 1"
    assert xs.scatterers().size() == len(poscar.sites)
Esempio n. 5
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def run(args):
  import iotbx.phil
  pcl = iotbx.phil.process_command_line(args=args, master_string="""\
symmetry_search {
  structure_factor_d_min = 2
    .type = float
}
""")
  if (len(pcl.remaining_args) != 1):
    from libtbx.utils import Usage
    import libtbx.load_env
    print
    pcl.master.show()
    print
    raise Usage(
      "%s pdb_file|poscar_file [parameters]" % libtbx.env.dispatcher_name)
  inp_file = pcl.remaining_args[0]
  from libtbx.str_utils import show_string
  import iotbx.pdb
  if (iotbx.pdb.is_pdb_file(inp_file)):
    print "PDB file:", show_string(inp_file)
    pdb_inp = iotbx.pdb.input(file_name=inp_file)
    xs = pdb_inp.xray_structure_simple()
  else:
    print "POSCAR file:", show_string(inp_file)
    import iotbx.poscar
    poscar = iotbx.poscar.reader(lines=open(inp_file).read().splitlines())
    poscar.make_up_types_if_necessary()
    xs = poscar.xray_structure()
  print
  pcl.work.show()
  print
  params = pcl.work.extract().symmetry_search
  print "Unit cell:", xs.unit_cell()
  print
  fc_p1 = xs.structure_factors(
    d_min=params.structure_factor_d_min).f_calc().expand_to_p1()
  from cctbx import symmetry_search
  sf_symm = symmetry_search.structure_factor_symmetry(f_in_p1=fc_p1)
  print sf_symm
  print
  print sf_symm.space_group_info
  print