dara package

Subpackages

• dara.bgmn package
  • Submodules
    • dara.bgmn.download_bgmn module
      • download_bgmn()
  • Module contents
• dara.data package
  • Module contents
• dara.prediction package
  • Submodules
    • dara.prediction.base module
      • PredictionEngine
    • dara.prediction.core module
      • PhasePredictor
    • dara.prediction.rn module
      • ReactionNetworkEngine
      • get_entry_by_formula()
    • dara.prediction.rxn_ca module
      • CellularAutomatonEngine
  • Module contents
• dara.search package
  • Submodules
    • dara.search.core module
      • remote_expand_node()
      • search_phases()
    • dara.search.data_model module
      • SearchNodeData
      • SearchResult
    • dara.search.peak_matcher module
      • PeakMatcher
      • absolute_log_error()
      • distance_matrix()
      • find_best_match()
      • merge_peaks()
    • dara.search.tree module
      • BaseSearchTree
      • SearchTree
      • batch_peak_matching()
      • batch_refinement()
      • calculate_fom_and_strain()
      • get_natural_break_results()
      • group_phases()
      • remove_unnecessary_phases()
  • Module contents
• dara.server package
  • Submodules
    • dara.server.api_router module
      • get_all_tasks()
      • plot()
      • result()
      • submit()
    • dara.server.app module
      • launch_app()
      • launch_worker_process()
    • dara.server.setting module
      • DaraServerSettings
      • get_dara_server_settings()
    • dara.server.utils module
      • convert_to_local_tz()
      • get_job_store()
      • get_result_store()
      • get_store()
      • get_worker_store()
    • dara.server.worker module
      • add_job_to_queue()
      • get_all_pending_jobs()
      • mark_running_jobs_as_fizzled()
      • run_job()
      • worker_process()
  • Module contents

Submodules

• dara.bgmn_worker module
  • BGMNWorker
    • BGMNWorker.run_refinement_cmd()
• dara.cif module
  • Cif
    • Cif.from_file()
    • Cif.from_str()
    • Cif.from_structure()
    • Cif.get_disordered_cifs()
    • Cif.get_disordered_structures()
    • Cif.name
    • Cif.to_file()
    • Cif.to_scaled_structure()
    • Cif.to_structure()
  • CifBlock
  • get_formula_with_disorder()
• dara.cif2str module
  • CIF2StrError
  • check_wyckoff()
  • cif2str()
  • get_lattice_parameters_from_lattice()
  • get_std_position()
  • make_lattice_parameters_str()
  • make_peak_parameter_str()
  • make_spacegroup_setting_str()
  • process_specie_string()
• dara.cli module
  • DaraCli
    • DaraCli.server
    • DaraCli.cli_cmd()
  • Server
    • Server.cli_cmd()
  • main()
• dara.eflech_worker module
  • EflechWorker
    • EflechWorker.generate_control_file()
    • EflechWorker.get_background_breakpoints()
    • EflechWorker.parse_par_file()
    • EflechWorker.parse_peak_list()
    • EflechWorker.patch_control_file_after_teil()
    • EflechWorker.run_eflech()
    • EflechWorker.run_peak_detection()
• dara.generate_control_file module
  • copy_instrument_files()
  • copy_xy_pattern()
  • generate_control_file()
  • trim_pattern()
• dara.jobs module
  • PhaseSearchMaker
    • PhaseSearchMaker.cifs_folder_name
    • PhaseSearchMaker.make()
    • PhaseSearchMaker.max_num_results
    • PhaseSearchMaker.name
    • PhaseSearchMaker.phase_predictor
    • PhaseSearchMaker.run_final_refinement
    • PhaseSearchMaker.verbose
  • RefinementMaker
    • RefinementMaker.make()
    • RefinementMaker.name
    • RefinementMaker.refinement_params
    • RefinementMaker.save
    • RefinementMaker.show_progress
• dara.peak_detection module
  • detect_peaks()
• dara.plot module
  • visualize()
• dara.refine module
  • RefinementPhase
    • RefinementPhase.params
    • RefinementPhase.path
    • RefinementPhase.make()
  • do_refinement()
  • do_refinement_no_saving()
• dara.result module
  • DiaResult
    • DiaResult.structs
    • DiaResult.x
    • DiaResult.y_bkg
    • DiaResult.y_calc
    • DiaResult.y_obs
  • LstResult
    • LstResult.d
    • LstResult.num_steps
    • LstResult.pattern_name
    • LstResult.phases_results
    • LstResult.r
    • LstResult.raw_lst
    • LstResult.rexp
    • LstResult.rho
    • LstResult.rp
    • LstResult.rpb
    • LstResult.rwp
  • ParseError
  • PhaseResult
    • PhaseResult.a
    • PhaseResult.alpha
    • PhaseResult.atom_positions_string
    • PhaseResult.b
    • PhaseResult.beta
    • PhaseResult.c
    • PhaseResult.gamma
    • PhaseResult.gewicht
    • PhaseResult.gewicht_name
    • PhaseResult.hermann_mauguin
    • PhaseResult.rphase
    • PhaseResult.spacegroup_no
    • PhaseResult.unit
    • PhaseResult.xray_density
    • PhaseResult.check_gewicht
    • PhaseResult.get_structure()
  • RefinementResult
    • RefinementResult.lst_data
    • RefinementResult.peak_data
    • RefinementResult.plot_data
    • RefinementResult.export_structure()
    • RefinementResult.get_phase_weights()
    • RefinementResult.transform
    • RefinementResult.visualize()
  • get_result()
  • parse_dia()
  • parse_lst()
  • parse_par()
• dara.schema module
  • PhaseSearchDocument
    • PhaseSearchDocument.best_rwp
    • PhaseSearchDocument.cifs_folder_name
    • PhaseSearchDocument.extra_peaks
    • PhaseSearchDocument.final_refinement_params
    • PhaseSearchDocument.final_result
    • PhaseSearchDocument.foms
    • PhaseSearchDocument.grouped_phases
    • PhaseSearchDocument.input_cifs
    • PhaseSearchDocument.last_updated
    • PhaseSearchDocument.lattice_strains
    • PhaseSearchDocument.missing_peaks
    • PhaseSearchDocument.phase_predictor
    • PhaseSearchDocument.precursors
    • PhaseSearchDocument.predict_kwargs
    • PhaseSearchDocument.results
    • PhaseSearchDocument.run_final_refinement
    • PhaseSearchDocument.search_kwargs
    • PhaseSearchDocument.task_label
    • PhaseSearchDocument.xrd_data
  • RefinementDocument
    • RefinementDocument.instrument_name
    • RefinementDocument.last_updated
    • RefinementDocument.phase_params
    • RefinementDocument.refinement_params
    • RefinementDocument.result
    • RefinementDocument.rwp
    • RefinementDocument.task_label
    • RefinementDocument.xrd_data
• dara.settings module
  • DaraSettings
    • DaraSettings.CONFIG_FILE
    • DaraSettings.PATH_TO_COD
    • DaraSettings.PATH_TO_ICSD
    • DaraSettings.load_default_settings
• dara.structure_db module
  • CODDatabase
    • CODDatabase.default_folder_path
    • CODDatabase.download_structures()
    • CODDatabase.get_file_path()
    • CODDatabase.name
  • ICSDDatabase
    • ICSDDatabase.default_folder_path
    • ICSDDatabase.download_structures()
    • ICSDDatabase.get_file_path()
    • ICSDDatabase.name
  • StructureDatabase
    • StructureDatabase.default_folder_path
    • StructureDatabase.download_structures()
    • StructureDatabase.get_cifs_by_chemsys()
    • StructureDatabase.get_cifs_by_formulas()
    • StructureDatabase.get_file_path()
    • StructureDatabase.get_formula_data()
    • StructureDatabase.local_copy_found
    • StructureDatabase.name
    • StructureDatabase.path
    • StructureDatabase.preparsed_info
• dara.utils module
  • angular_correction()
  • bool2yn()
  • compositions_to_array()
  • copy_and_rename_files()
  • datetime_str()
  • find_optimal_intensity_threshold()
  • find_optimal_score_threshold()
  • fuzzy_compare()
  • get_chemsys_from_formulas()
  • get_composition_distance()
  • get_composition_from_filename()
  • get_compositional_clusters()
  • get_entries_db()
  • get_entries_in_chemsys_db()
  • get_entries_in_chemsys_mp()
  • get_head_of_compositional_cluster()
  • get_logger()
  • get_number()
  • get_optimal_max_two_theta()
  • get_wavelength()
  • intensity_correction()
  • load_symmetrized_structure()
  • parse_refinement_param()
  • process_phase_name()
  • read_phase_name_from_str()
  • rpb()
  • rwp()
  • standardize_coords()
• dara.xrd module
  • RASXFile
    • RASXFile.binary_data
    • RASXFile.from_file()
    • RASXFile.to_rasx_file()
  • RawFile
    • RawFile.binary_data
    • RawFile.from_file()
    • RawFile.to_raw_file()
  • XRDData
    • XRDData.angles
    • XRDData.errors
    • XRDData.from_file()
    • XRDData.intensities
    • XRDData.plot()
    • XRDData.to_xy_file()
  • XRDMLFile
    • XRDMLFile.from_file()
    • XRDMLFile.to_xrdml_file()
    • XRDMLFile.xrdml_dict
  • XYFile
    • XYFile.from_file()
  • get_xrdml_data()
  • hex2float()
  • hex2int()
  • load_rasx()
  • load_raw()
  • load_xrdml()
  • rasx2xy()
  • raw2xy()
  • xrdml2xy()

Module contents

Automatically configures DARA settings.