from __future__ import absolute_import, division, print_function import iotbx.phil from libtbx.test_utils import show_diff, Exception_expected from libtbx.utils import Sorry from libtbx import Auto import os def exercise(): master = iotbx.phil.parse(input_string="""\ u=10,12 13 80,90 100 .type=unit_cell s=19 .type=space_group U=None .type=unit_cell S=None .type=space_group ua=Auto .type=unit_cell sa=Auto .type=space_group """) assert not show_diff(master.format(master.extract()).as_str(), """\ u = 10 12 13 80 90 100 s = "P 21 21 21" U = None S = None ua = Auto sa = Auto """) custom = iotbx.phil.parse(input_string="""\ ua = None s = Auto U = 1,2,3 u = Auto S = 33 sa = None """) assert not show_diff( master.fetch(source=custom).extract_format().as_str(), """\ u = Auto s = Auto U = 1 2 3 90 90 90 S = "P n a 21" ua = None sa = None """) # make sure Unicode strings work! custom = iotbx.phil.parse(input_string=u"""\ U = 1 2 3 90 105 90 S = P21 """) assert not show_diff( master.fetch(source=custom).extract_format().as_str(), """\ u = 10 12 13 80 90 100 s = "P 21 21 21" U = 1 2 3 90 105 90 S = "P 1 21 1" ua = Auto sa = Auto """) # master = iotbx.phil.parse(input_string="""\ s=None .type=space_group .multiple=True """) custom = iotbx.phil.parse(input_string="""\ s=p212121 s=19 """) assert not show_diff(master.fetch(source=custom).as_str(), """\ s = 19 """) custom = iotbx.phil.parse(input_string="""\ s=19 s=p212121 """) assert not show_diff(master.fetch(source=custom).as_str(), """\ s = p212121 """) custom = iotbx.phil.parse(input_string="""\ s=18 s=p212121 """) assert not show_diff(master.fetch(source=custom).as_str(), """\ s = 18 s = p212121 """) # master = iotbx.phil.parse(input_string="""\ sel = None .type = atom_selection .multiple = True """) clai = master.command_line_argument_interpreter() assert not show_diff(clai.process( "sel=altloc ' ' or name C\\* ").as_str(), """\ sel = altloc ' ' or name C\\* """) user = iotbx.phil.parse(input_string="""\ sel = "altloc ' ' or name C\\*" sel = altloc ' ' or name D\\* """) work = master.fetch(user) assert not show_diff(work.as_str(), """\ sel = "altloc ' ' or name C\\\\*" sel = altloc ' ' or name D\\* """) ex = work.extract() assert len(ex.sel) == 2 assert ex.sel[0] == "altloc ' ' or name C\\*" assert ex.sel[1] == "altloc ' ' or name D\\*" # pcl = iotbx.phil.process_command_line(args=["s = 230"], master_string="""\ s=None .type=space_group """) assert not show_diff(str(pcl.work.extract().s), "I a -3 d") # master_phil_str = """ model = None .type = path use_geometry_restraints = False .type = bool """ with open("model.pdb", "w") as f: f.write("""\ ATOM 1 O HOH 1 53.448 18.599 -10.134 1.00 20.00 """) pcl = iotbx.phil.process_command_line_with_files( args=["model.pdb", "--use_geometry_restraints"], master_phil_string=master_phil_str, pdb_file_def="model") assert (pcl.get_file_type_count("pdb") == 1) assert (pcl.get_file_type_count("hkl") == 0) params = pcl.work.extract() pdb_in = pcl.get_cached_file(params.model) assert (pdb_in is not None) assert (params.model == os.path.join(os.getcwd(), "model.pdb")) assert (params.use_geometry_restraints) model_in = pcl.get_file(params.model, force_type="pdb") master_phil_str = """ data_dir = None .type = path d_min = None .type = float nproc = None .type = int """ pcl = iotbx.phil.process_command_line_with_files( args=["/", "3.0", "5"], master_phil_string=master_phil_str, directory_def="data_dir", integer_def="nproc", float_def="d_min") params = pcl.work.extract() assert (params.data_dir == "/") assert (params.d_min == 3.0) assert (params.nproc == 5) # shelx file hack with open("tst_iotbx_phil.hkl", "w") as f: f.write("""\ 1 2 -1 -23.34 4.56 1 2 -3 9 12.45 6.12 2 99999999999999999.9999999.999999 -999-999-999-9999.99-9999.99-999 0 0 0 0.00 0.00 0""") master_phil_str = """ data = None .type = path space_group = None .type = space_group unit_cell = None .type = unit_cell """ pcl = iotbx.phil.process_command_line_with_files( args=[ "tst_iotbx_phil.hkl", "P6122", "50,50,40,90,90,120", ], master_phil_string=master_phil_str, reflection_file_def="data", space_group_def="space_group", unit_cell_def="unit_cell") params = pcl.work.extract() assert (str(params.space_group) == "P 61 2 2") assert (str(params.unit_cell) == "(50, 50, 40, 90, 90, 120)") from iotbx.file_reader import any_file try : hkl_in = any_file(params.data, force_type="hkl") print(hkl_in.file_server.miller_arrays[0].is_xray_intensity_array()) except Sorry as s : assert ("Unresolved amplitude/intensity ambiguity" in str(s)) else : raise Exception_expected pcl = iotbx.phil.process_command_line_with_files( args=["tst_iotbx_phil.hkl=hklf3"], master_phil_string=master_phil_str, reflection_file_def="data") params = pcl.work.extract() assert (params.data == "tst_iotbx_phil.hkl=hklf3") hkl_in = any_file(params.data, force_type="hkl") ma = hkl_in.file_server.miller_arrays[0] assert ma.is_xray_amplitude_array() assert ma.anomalous_flag() is False with open("tst_iotbx_phil.ncs", "w") as f: f.write(""" REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.623490 0.781831 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.781831 0.623490 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 """) master_phil_str = """ ncs_file = None .type = path """ pcl = iotbx.phil.process_command_line_with_files( args=[ "tst_iotbx_phil.ncs", ], master_phil_string=master_phil_str, ncs_file_def="ncs_file") params = pcl.work.extract() assert (os.path.split(str(params.ncs_file))[-1] == "tst_iotbx_phil.ncs") with open("tst_iotbx_phil.ncs_spec", "w") as f: f.write(""" Summary of NCS information Wed Mar 16 15:02:22 2016 /Users/terwill/Desktop/working/Jan_2015/phenix/cryo-pdb/3j9c/build source_info ncs_biomtr.ncs new_ncs_group new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 0.0000 0.0000 0.0000 new_operator rota_matrix 0.6235 -0.7818 0.0000 rota_matrix 0.7818 0.6235 -0.0000 rota_matrix -0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 """) master_phil_str = """ ncs_file = None .type = path """ pcl = iotbx.phil.process_command_line_with_files( args=[ "tst_iotbx_phil.ncs_spec", ], master_phil_string=master_phil_str, ncs_file_def="ncs_file") params = pcl.work.extract() assert (os.path.split(str(params.ncs_file))[-1] == "tst_iotbx_phil.ncs_spec") print("OK") if (__name__ == "__main__"): exercise()