iotbx.xds¶
Overview¶
API documentation¶
- class iotbx.xds.xds_inp.reader¶
A class to read the XDS.INP file used in XDS
- static is_xds_inp_file(filename)¶
Check if the given file is an XDS.INP file.
- Params:
filename The XDS.INP filename
- Returns:
True/False the file is a XDS.INP file
- parse_lines(lines)¶
Parse the lines
- Param:
tokens The list of lines
- read_file(filename, check_filename=True)¶
Read the XDS.INP file.
See http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_files.html for more information about the file format.
- Param:
filename The path to the file
- class iotbx.xds.xparm.reader¶
A class to read the XPARM.XDS/GXPARM.XDS file used in XDS
- static find_version(filename)¶
Check the version if the given file is a (G)XPARM.XDS file.
If the file contains exactly 11 lines and 42 tokens, it is the old style version 1 file. If the file starts with XPARM.XDS it is the new style version 2 file. If the file contains segment definitions then it is a version 3 file.
- Params:
filename The (G)XPARM.XDS filename
- Returns:
The version or None if the file is not recognised
- static is_xparm_file(filename, check_filename=True)¶
Check if the given file is a (G)XPARM.XDS file.
Ensure it is named correctly and contains exactly 11 lines and 42 tokens, otherwise return False.
- Params:
filename The (G)XPARM.XDS filename
- Returns:
True/False the file is a (G)XPARM.XDS file
- parse_version_1_tokens(tokens)¶
Parse the version 1 tokens
- Param:
tokens The list of tokens
- parse_version_2_tokens(tokens)¶
Parse the version 2 tokens
- Param:
tokens The list of tokens
- read_file(filename, check_filename=True)¶
Read the XPARM.XDS/GXPARAM.XDS file.
See http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_files.html for more information about the file format.
- Param:
filename The path to the file
- iotbx.xds.xparm.write(starting_frame, starting_angle, oscillation_range, rotation_axis, wavelength, beam_vector, space_group, unit_cell, unit_cell_a_axis, unit_cell_b_axis, unit_cell_c_axis, num_segments, detector_size, pixel_size, detector_origin, detector_distance, detector_x_axis, detector_y_axis, detector_normal, segments=None, orientation=None)¶
- class iotbx.xds.xparm.writer(starting_frame, starting_angle, oscillation_range, rotation_axis, wavelength, beam_vector, space_group, unit_cell, unit_cell_a_axis, unit_cell_b_axis, unit_cell_c_axis, num_segments, detector_size, pixel_size, detector_origin, detector_distance, detector_x_axis, detector_y_axis, detector_normal, segments=None, orientation=None)¶
-
- write_file(filename)¶
- iotbx.xds.read_ascii.get_rhs(line)¶
- class iotbx.xds.read_ascii.reader(file_handle, header_only=False, allow_unmerged=True)¶
- as_miller_array(crystal_symmetry=None, force_symmetry=False, merge_equivalents=True, base_array_info=None, anomalous=None)¶
- as_miller_arrays(crystal_symmetry=None, force_symmetry=False, merge_equivalents=True, base_array_info=None, anomalous=None)¶
- batch_as_miller_array(crystal_symmetry=None, force_symmetry=False, base_array_info=None)¶
- column_index(line)¶
- crystal_symmetry()¶
- miller_set(crystal_symmetry=None, force_symmetry=False, anomalous=None)¶
- class iotbx.xds.spot_xds.reader¶
Class to read the SPOT.XDS file.
- read_file(filename)¶
Read the spot file.
- class iotbx.xds.spot_xds.writer(centroids, intensities, miller_indices=None)¶
Class to write the SPOT.XDS file.
- write_file(filename=None)¶
Write the spot file.
- class iotbx.xds.integrate_hkl.reader¶
A class to read the INTEGRATE.HKL file used in XDS
- as_miller_arrays(crystal_symmetry=None, force_symmetry=False, merge_equivalents=True, base_array_info=None, anomalous=None)¶
- static is_integrate_hkl_file(filename)¶
Check that the file is identified as an INTEGRATE.HKL
- Params:
filename The path to the file
- Returns:
True/False Is the file an INTEGRATE.HKL file
- read_file(filename)¶
Read the INTEGRATE.HKL file.
See http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_files.html for more information about the file format.
- Params:
filename The path to the file