from __future__ import absolute_import, division, print_function from cctbx import crystal from libtbx.utils import Sorry, date_and_time, multi_out import iotbx.phil from iotbx import reflection_file_reader from iotbx import reflection_file_utils from iotbx import crystal_symmetry_from_any import mmtbx.scaling from mmtbx.scaling import pair_analyses from libtbx.str_utils import StringIO from mmtbx.scaling import pre_scale, make_param import sys, os from mmtbx.scaling import fa_estimation params_generator = make_param.phil_lego() master_params = iotbx.phil.parse( params_generator.default_2wmad() ) def run(args): if len(args)==0: master_params.show(expert_level=100) elif ( "--help" in args ): print("no help available") elif ( "--h" in args ): print("no help available") elif ( "--show_defaults" in args ): master_params.show(expert_level=0) elif ( "--show_defaults_all" in args ): master_params.show(expert_level=10) else: log = multi_out() if (not "--quiet" in args): log.register(label="stdout", file_object=sys.stdout) string_buffer = StringIO() string_buffer_plots = StringIO() log.register(label="log_buffer", file_object=string_buffer) log_plots = StringIO() print("#phil __OFF__", file=log) print(file=log) print(date_and_time(), file=log) print(file=log) print(file=log) phil_objects = [] argument_interpreter = master_params.command_line_argument_interpreter( home_scope="scaling") reflection_file = None for arg in args: command_line_params = None arg_is_processed = False if arg == '--quiet': arg_is_processed = True ## The associated action with this keyword is implemented above if (os.path.isfile(arg)): ## is this a file name? ## Check if this is a phil file try: command_line_params = iotbx.phil.parse(file_name=arg) except KeyboardInterrupt: raise except Exception : pass if command_line_params is not None: phil_objects.append(command_line_params) arg_is_processed = True ## Check if this file is a reflection file if command_line_params is None: reflection_file = reflection_file_reader.any_reflection_file( file_name=arg, ensure_read_access=False) if (reflection_file is not None): reflection_file = arg arg_is_processed = True ## If it is not a file, it must be a phil command else: try: command_line_params = argument_interpreter.process(arg=arg) if command_line_params is not None: phil_objects.append(command_line_params) arg_is_processed = True except KeyboardInterrupt: raise except Exception : pass if not arg_is_processed: print("##----------------------------------------------##", file=log) print("## Unknown phil-file or phil-command:", arg, file=log) print("##----------------------------------------------##", file=log) print(file=log) raise Sorry("Unknown file format or phil command: %s" % arg) effective_params = master_params.fetch(sources=phil_objects) params = effective_params.extract() ## Now please read in the reflections files ## get symmetry and cell data first please ## By default, the native cell and symmetry are used ## as reference crystal_symmetry_nat = None print(params.scaling.input.xray_data.wavelength1.file_name) crystal_symmetry_nat = crystal_symmetry_from_any.extract_from( file_name=params.scaling.input.xray_data.wavelength1.file_name) if params.scaling.input.xray_data.space_group is None: params.scaling.input.xray_data.space_group =\ crystal_symmetry_nat.space_group_info() print("Using symmetry of native data", file=log) if params.scaling.input.xray_data.unit_cell is None: params.scaling.input.xray_data.unit_cell =\ crystal_symmetry_nat.unit_cell() print("Using cell of native data", file=log) ## Check if a unit cell is defined if params.scaling.input.xray_data.space_group is None: raise Sorry("No space group defined") if params.scaling.input.xray_data.unit_cell is None: raise Sorry("No unit cell defined") crystal_symmetry = crystal_symmetry = crystal.symmetry( unit_cell = params.scaling.input.xray_data.unit_cell, space_group_symbol = str( params.scaling.input.xray_data.space_group) ) effective_params = master_params.fetch(sources=phil_objects) new_params = master_params.format(python_object=params) print("Effective parameters", file=log) print("#phil __ON__", file=log) new_params.show(out=log,expert_level=params.scaling.input.expert_level) print("#phil __END__", file=log) print(file=log) ## define a xray data server xray_data_server = reflection_file_utils.reflection_file_server( crystal_symmetry = crystal_symmetry, force_symmetry = True, reflection_files=[]) ## Read in native data and make appropriate selections miller_array_w1 = None miller_array_w1 = xray_data_server.get_xray_data( file_name = params.scaling.input.xray_data.wavelength1.file_name, labels = params.scaling.input.xray_data.wavelength1.labels, ignore_all_zeros = True, parameter_scope = 'scaling.input.SIR_scale.xray_data.native' ) info_native = miller_array_w1.info() miller_array_w1=miller_array_w1.map_to_asu().select( miller_array_w1.indices()!=(0,0,0) ) miller_array_w1 = miller_array_w1.select( miller_array_w1.data() > 0 ) ## Convert to amplitudes if (miller_array_w1.is_xray_intensity_array()): miller_array_w1 = miller_array_w1.f_sq_as_f() elif (miller_array_w1.is_complex_array()): miller_array_w1 = abs(miller_array_w1) if not miller_array_w1.is_real_array(): raise Sorry("miller_array_native is not a real array") miller_array_w1.set_info(info = info_native) ## Read in derivative data and make appropriate selections miller_array_w2 = None miller_array_w2 = xray_data_server.get_xray_data( file_name = params.scaling.input.xray_data.wavelength2.file_name, labels = params.scaling.input.xray_data.wavelength2.labels, ignore_all_zeros = True, parameter_scope = 'scaling.input.SIR_scale.xray_data.derivative' ) info_w2 = miller_array_w2.info() miller_array_w2=miller_array_w2.map_to_asu().select( miller_array_w2.indices()!=(0,0,0) ) miller_array_w2 = miller_array_w2.select( miller_array_w2.data() > 0 ) ## Convert to amplitudes if (miller_array_w2.is_xray_intensity_array()): miller_array_w2 = miller_array_w2.f_sq_as_f() elif (miller_array_w2.is_complex_array()): miller_array_w2 = abs(miller_array_w2) if not miller_array_w2.is_real_array(): raise Sorry("miller_array_derivative is not a real array") miller_array_w2.set_info(info = info_w2) ## Make sure we have anomalous diffs in both files assert miller_array_w1.anomalous_flag() assert miller_array_w2.anomalous_flag() ## Print info print(file=log) print("Wavelength 1", file=log) print("============", file=log) miller_array_w1.show_comprehensive_summary(f=log) print(file=log) w1_pre_scale = pre_scale.pre_scaler( miller_array_w1, params.scaling.input.scaling_strategy.pre_scaler_protocol, params.scaling.input.basic) miller_array_w1 = w1_pre_scale.x1.deep_copy() del w1_pre_scale print(file=log) print("Wavelength 2", file=log) print("============", file=log) miller_array_w2.show_comprehensive_summary(f=log) print(file=log) w2_pre_scale = pre_scale.pre_scaler( miller_array_w2, params.scaling.input.scaling_strategy.pre_scaler_protocol, params.scaling.input.basic) miller_array_w2 = w2_pre_scale.x1.deep_copy() del w2_pre_scale print(file=log) print("Checking for possible reindexing schemes", file=log) print("----------------------------------------", file=log) print(file=log) print("Reindexing operator derived as described in:", file=log) print("Grosse-Kunstleve, Afonine, Sauter & Adams. (2005).", file=log) print(" IUCr Computing Commission Newsletter 5.", file=log) print(file=log) reindex_object = pair_analyses.reindexing( set_a=miller_array_w1, set_b=miller_array_w2, out=log) miller_array_w2 = reindex_object.select_and_transform() miller_array_w2.map_to_asu() print(file=log) print("Relative scaling of 2-wavelength mad data", file=log) print("-----------------------------------------", file=log) print(file=log) scaler = fa_estimation.combined_scaling( miller_array_w1, miller_array_w2, params.scaling.input.scaling_strategy.iso_protocol) miller_array_w1 = scaler.x1.deep_copy() miller_array_w2 = scaler.x2.deep_copy() del scaler print(file=log) print("Estimating f\" and f' ratios", file=log) print("----------------------------", file=log) print(file=log) # now things are scaled see if we can guestimate the ratio fdpratio = pair_analyses.f_double_prime_ratio( miller_array_w1, miller_array_w2) fpfdpratio = pair_analyses.delta_f_prime_f_double_prime_ratio( miller_array_w1, miller_array_w2) k1 = fdpratio.ratio k2 = fpfdpratio.ratio if k1 is not None: print(file=log) print(" The estimate of f\"(w1)/f\"(w2) is %3.2f"\ %(fdpratio.ratio), file=log) if k2 is not None: print(" The estimate of (f'(w1)-f'(w2))/f\"(w2) is %3.2f"\ %(fpfdpratio.ratio), file=log) print(file=log) print(" The quality of these estimates depends to a large extend", file=log) print(" on the quality of the data. If user supplied values", file=log) print(" of f\" and f' are given, they will be used instead ", file=log) print(" of the estimates.", file=log) print(file=log) if params.scaling.input.xray_data.wavelength1.f_double_prime is not None: if params.scaling.input.xray_data.wavelength2.f_double_prime is not None: k1 = (params.scaling.input.xray_data.wavelength1.f_double_prime/ params.scaling.input.xray_data.wavelength2.f_double_prime) print(" Using user specified f\" values", file=log) print(" user specified f\"(w1)/f\"(w2) is %3.2f"\ %(k1), file=log) print(file=log) if params.scaling.input.xray_data.wavelength1.f_prime is not None: if params.scaling.input.xray_data.wavelength2.f_prime is not None: if params.scaling.input.xray_data.wavelength2.f_double_prime is not None: k2 = (params.scaling.input.xray_data.wavelength1.f_prime- params.scaling.input.xray_data.wavelength2.f_prime)\ /params.scaling.input.xray_data.wavelength2.f_double_prime print(" Using user specified f\" and f' values", file=log) print(" user specified f\"(w1)/f\"(w2) is %3.2f"\ %(k2), file=log) print(file=log) fa_gen = fa_estimation.twmad_fa_driver(miller_array_w1, miller_array_w2, k1, k2, params.scaling.input.fa_estimation) print(file=log) print("writing mtz file", file=log) print("----------------", file=log) print(file=log) ## Please write out the abs_delta_f array fa = fa_gen.fa_values mtz_dataset = fa.as_mtz_dataset( column_root_label='F'+params.scaling.input.output.outlabel) mtz_dataset.mtz_object().write( file_name=params.scaling.input.output.hklout) if (__name__ == "__main__"): run(sys.argv[1:])