Python reflnlist Examples

Example #1

File: crystal_symmetry_from_ref.py Project: zhuligs/cctbx_project

def extract_from(file_name):
    return reflnlist_reader.reflnlist(open(file_name),
                                      header_only=True).crystal_symmetry()

Example #2

File: reflection_file_reader.py Project: cctbx/cctbx-playground

def try_all_readers(file_name):
  try: content = mtz.object(file_name=file_name)
  except RuntimeError: pass
  else: return ("ccp4_mtz", content)
  if (detect_binary_file.from_initial_block(file_name=file_name)):
    try: content = unpickle_miller_arrays(file_name=file_name)
    except KeyboardInterrupt: raise
    except Exception: pass
    else: return ("cctbx.miller.array", content)
    return (None, None)
  try: content = cns_reflection_reader.cns_reflection_file(
    open(file_name))
  except cns_reflection_reader.CNS_input_Error: pass
  else: return ("cns_reflection_file", content)
  try: content = cns_index_fobs_sigma_reader.reader(
    file_name=file_name)
  except RuntimeError: pass
  else: return ("cns_index_fobs_sigma", content)
  try: content = scalepack_merge.reader(
    open(file_name))
  except scalepack_merge.FormatError: pass
  else: return ("scalepack_merge", content)
  try: content = scalepack_no_merge.reader(file_name)
  except KeyboardInterrupt: raise
  except Exception: pass
  else: return ("scalepack_no_merge_original_index", content)
  try: content = dtrek_reflnlist_reader.reflnlist(
    open(file_name))
  except KeyboardInterrupt: raise
  except Exception: pass
  else: return ("dtrek_reflnlist", content)
  try: content = shelx_hklf.reader(
    file_name=file_name)
  except KeyboardInterrupt: raise
  except Exception: pass
  else: return ("shelx_hklf", content)
  try:
    content = cif_reader(file_path=file_name)
    looks_like_a_reflection_file = False
    for block in content.model().values():
      if '_refln_index_h' in block or '_refln.index_h' in block:
        looks_like_a_reflection_file = True
        break
    if not looks_like_a_reflection_file:
      raise RuntimeError
  except KeyboardInterrupt: raise
  except Exception: pass
  else: return ("cif", content)
  try: content = xds_ascii_reader(
    open(file_name))
  except KeyboardInterrupt: raise
  except Exception: pass
  else: return ("xds_ascii", content)
  try:
    content = xds_integrate_hkl_reader()
    content.read_file(file_name)
  except KeyboardInterrupt: raise
  except Exception: pass
  else: return ("xds_integrate_hkl", content)
  try: content = solve_fpfm_reader(file_name=file_name)
  except KeyboardInterrupt: raise
  except Exception: pass
  else: return ("solve_fpfm", content)
  return (None, None)

Example #3

File: crystal_symmetry_from_ref.py Project: cctbx/cctbx-playground

def extract_from(file_name):
  return reflnlist_reader.reflnlist(
    open(file_name), header_only=True).crystal_symmetry()

Example #4

def try_all_readers(file_name):
    try:
        content = mtz.object(file_name=file_name)
    except RuntimeError:
        pass
    else:
        return ("ccp4_mtz", content)
    if (detect_binary_file.from_initial_block(file_name=file_name)):
        try:
            content = unpickle_miller_arrays(file_name=file_name)
        except KeyboardInterrupt:
            raise
        except Exception:
            pass
        else:
            return ("cctbx.miller.array", content)
        return (None, None)
    try:
        content = cns_reflection_reader.cns_reflection_file(open(file_name))
    except cns_reflection_reader.CNS_input_Error:
        pass
    else:
        return ("cns_reflection_file", content)
    try:
        content = cns_index_fobs_sigma_reader.reader(file_name=file_name)
    except RuntimeError:
        pass
    else:
        return ("cns_index_fobs_sigma", content)
    try:
        content = scalepack_merge.reader(open(file_name))
    except scalepack_merge.FormatError:
        pass
    else:
        return ("scalepack_merge", content)
    try:
        content = scalepack_no_merge.reader(file_name)
    except KeyboardInterrupt:
        raise
    except Exception:
        pass
    else:
        return ("scalepack_no_merge_original_index", content)
    try:
        content = dtrek_reflnlist_reader.reflnlist(open(file_name))
    except KeyboardInterrupt:
        raise
    except Exception:
        pass
    else:
        return ("dtrek_reflnlist", content)
    try:
        content = shelx_hklf.reader(file_name=file_name)
    except KeyboardInterrupt:
        raise
    except Exception:
        pass
    else:
        return ("shelx_hklf", content)
    try:
        content = cif_reader(file_path=file_name)
        looks_like_a_reflection_file = False
        for block in content.model().values():
            if '_refln_index_h' in block or '_refln.index_h' in block:
                looks_like_a_reflection_file = True
                break
        if not looks_like_a_reflection_file:
            raise RuntimeError
    except KeyboardInterrupt:
        raise
    except Exception:
        pass
    else:
        return ("cif", content)
    try:
        content = xds_ascii_reader(open(file_name))
    except KeyboardInterrupt:
        raise
    except Exception:
        pass
    else:
        return ("xds_ascii", content)
    try:
        content = xds_integrate_hkl_reader()
        content.read_file(file_name)
    except KeyboardInterrupt:
        raise
    except Exception:
        pass
    else:
        return ("xds_integrate_hkl", content)
    try:
        content = solve_fpfm_reader(file_name=file_name)
    except KeyboardInterrupt:
        raise
    except Exception:
        pass
    else:
        return ("solve_fpfm", content)
    return (None, None)

Example #5

def extract_from(file_name):
    with open(file_name) as f:
        cs = reflnlist_reader.reflnlist(f, header_only=True).crystal_symmetry()
    return cs