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_siras() ) def run(args): if len(args)==0: master_params.show(expert_level=0) elif ( "--help" in args ): print("no help available as yet") elif ( "--h" in args ): print("no help availableas yet") 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.native.file_name) crystal_symmetry_nat = crystal_symmetry_from_any.extract_from( file_name=params.scaling.input.xray_data.native.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=effective_params.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 appropriatre selections miller_array_native = None miller_array_native = xray_data_server.get_xray_data( file_name = params.scaling.input.xray_data.native.file_name, labels = params.scaling.input.xray_data.native.labels, ignore_all_zeros = True, parameter_scope = 'scaling.input.SIR_scale.xray_data.native' ) info_native = miller_array_native.info() miller_array_native=miller_array_native.map_to_asu().select( miller_array_native.indices()!=(0,0,0) ) miller_array_native = miller_array_native.select( miller_array_native.data() > 0 ) ## Convert to amplitudes if (miller_array_native.is_xray_intensity_array()): miller_array_native = miller_array_native.f_sq_as_f() elif (miller_array_native.is_complex_array()): miller_array_native = abs(miller_array_native) if not miller_array_native.is_real_array(): raise Sorry("miller_array_native is not a real array") miller_array_native.set_info(info = info_native) ## Read in derivative data and make appropriate selections miller_array_derivative = None miller_array_derivative = xray_data_server.get_xray_data( file_name = params.scaling.input.xray_data.derivative.file_name, labels = params.scaling.input.xray_data.derivative.labels, ignore_all_zeros = True, parameter_scope = 'scaling.input.SIR_scale.xray_data.derivative' ) info_derivative = miller_array_derivative.info() miller_array_derivative=miller_array_derivative.map_to_asu().select( miller_array_derivative.indices()!=(0,0,0) ) miller_array_derivative = miller_array_derivative.select( miller_array_derivative.data() > 0 ) ## Convert to amplitudes if (miller_array_derivative.is_xray_intensity_array()): miller_array_derivative = miller_array_derivative.f_sq_as_f() elif (miller_array_derivative.is_complex_array()): miller_array_derivative = abs(miller_array_derivative) if not miller_array_derivative.is_real_array(): raise Sorry("miller_array_derivative is not a real array") miller_array_derivative.set_info(info = info_derivative) ## Make sure we have anomalous diffs assert miller_array_derivative.anomalous_flag() ## As this is a SIR case, we will remove any anomalous pairs from the native if miller_array_native.anomalous_flag(): miller_array_native = miller_array_native.average_bijvoet_mates()\ .set_observation_type( miller_array_native ) ## Use this copy for anomalous diff's later miller_array_derivative_anom = miller_array_derivative.deep_copy() if miller_array_derivative.anomalous_flag(): miller_array_derivative = miller_array_derivative.average_bijvoet_mates()\ .set_observation_type( miller_array_derivative ) ## Print info print(file=log) print("Native data", file=log) print("===========", file=log) miller_array_native.show_comprehensive_summary(f=log) print(file=log) native_pre_scale = pre_scale.pre_scaler( miller_array_native, params.scaling.input.scaling_strategy.pre_scaler_protocol, params.scaling.input.basic) miller_array_native = native_pre_scale.x1.deep_copy() del native_pre_scale print(file=log) print("Derivative data (merged friedels)", file=log) print("=================================", file=log) miller_array_derivative.show_comprehensive_summary(f=log) print(file=log) derivative_pre_scale = pre_scale.pre_scaler( miller_array_derivative, params.scaling.input.scaling_strategy.pre_scaler_protocol, params.scaling.input.basic) miller_array_derivative = derivative_pre_scale.x1.deep_copy() del derivative_pre_scale print(file=log) print("Anomalous data (non merged Friedels of derivative)", file=log) print("==================================================", file=log) miller_array_derivative_anom.show_comprehensive_summary(f=log) print(file=log) derivative_anom_pre_scale = pre_scale.pre_scaler( miller_array_derivative_anom, params.scaling.input.scaling_strategy.pre_scaler_protocol, params.scaling.input.basic) miller_array_derivative_anom = derivative_anom_pre_scale.x1.deep_copy() print(file=log) print("Working on isomorphous differences", file=log) print("==================================", file=log) print(file=log) iso_scaler = fa_estimation.combined_scaling( miller_array_native, miller_array_derivative, params.scaling.input.scaling_strategy.iso_protocol) miller_array_native = iso_scaler.x1.deep_copy() miller_array_derivative = iso_scaler.x2.deep_copy() del iso_scaler delta_gen_iso = pair_analyses.delta_generator( miller_array_native, miller_array_derivative ) print(file=log) print("Working on anomalous differences", file=log) print("================================", file=log) print(file=log) ano_scaler = fa_estimation.ano_scaling( miller_array_derivative_anom, params.scaling.input.scaling_strategy.ano_protocol) positive_miller = ano_scaler.x1p.deep_copy() negative_miller = ano_scaler.x1n.deep_copy() del ano_scaler delta_gen_ano = pair_analyses.delta_generator( positive_miller, negative_miller) print(file=log) print("Combining iso and ano data", file=log) print("==========================", file=log) print(file=log) fa = fa_estimation.naive_fa_estimation( delta_gen_ano.abs_delta_f, delta_gen_iso.abs_delta_f, 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 mtz_dataset = fa.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:])