Python run_xia2_tolerant示例

示例#1

文件： tst_X4_wide.py 项目： xia2/xia2_regression

def exercise_xds_ccp4a():
  command_line_args = [
    'pipeline=3di', 'nproc=1', 'scaler=ccp4a', 'trust_beam_centre=True', data_dir]

  expected_data_files = [
    'AUTOMATIC_DEFAULT_free.mtz',
    'AUTOMATIC_DEFAULT_scaled.sca',
    'AUTOMATIC_DEFAULT_scaled_unmerged.mtz',
    'AUTOMATIC_DEFAULT_scaled_unmerged.sca']

  run_xia2_tolerant("X4_wide.ccp4a", command_line_args,
           expected_data_files=expected_data_files)

示例#2

文件： tst_X4_wide.py 项目： xia2/xia2_regression

def exercise_xds():
  command_line_args = ['pipeline=3di', 'nproc=1', 'trust_beam_centre=True',
                       'read_all_image_headers=False', data_dir]

  expected_data_files = [
    'AUTOMATIC_DEFAULT_free.mtz',
    'AUTOMATIC_DEFAULT_scaled.sca',
    'AUTOMATIC_DEFAULT_scaled_unmerged.mtz',
    'AUTOMATIC_DEFAULT_scaled_unmerged.sca']

  run_xia2_tolerant("X4_wide.xds", command_line_args,
           expected_data_files=expected_data_files)

示例#3

文件： tst_mad_example.py 项目： xia2/xia2_regression

def exercise_xds_ccp4a():
  command_line_args = [
    'pipeline=3di', 'scaler=ccp4a', 'nproc=1', 'njob=2', 'mode=parallel',
    'trust_beam_centre=True', data_dir]

  expected_data_files = [
    'AUTOMATIC_DEFAULT_free.mtz',
    'AUTOMATIC_DEFAULT_scaled_WAVE2.sca',
    'AUTOMATIC_DEFAULT_scaled_unmerged_WAVE1.sca',
    'AUTOMATIC_DEFAULT_scaled_unmerged_WAVE2.sca',
    'AUTOMATIC_DEFAULT_scaled_WAVE1.sca',
    'AUTOMATIC_DEFAULT_scaled_unmerged_WAVE1.mtz',
    'AUTOMATIC_DEFAULT_scaled_unmerged_WAVE2.mtz']

  run_xia2_tolerant("mad_example.ccp4a", command_line_args,
           expected_data_files=expected_data_files)

示例#4

文件： tst_X4_wide.py 项目： xia2/xia2_regression

def exercise_xds_split():
  tmp_dir = os.path.abspath(open_tmp_directory())
  xinfo_file = os.path.join(tmp_dir, 'split.xinfo')
  with open(xinfo_file, 'wb') as f:
    print >> f, split_xinfo_template

  command_line_args = ['pipeline=3di', 'nproc=1', 'njob=2', 'mode=parallel',
                       'trust_beam_centre=True', 'xinfo=%s' %xinfo_file]

  expected_data_files = [
    'AUTOMATIC_DEFAULT_free.mtz',
    'AUTOMATIC_DEFAULT_scaled.sca',
    'AUTOMATIC_DEFAULT_scaled_unmerged.mtz',
    'AUTOMATIC_DEFAULT_scaled_unmerged.sca']

  run_xia2_tolerant("X4_wide_split.xds", command_line_args,
           expected_data_files=expected_data_files)