Index

A

a (PhaseResult attribute) absolute_log_error() (in module dara.search.peak_matcher) add_job_to_queue() (in module dara.server.worker) add_subtree() (BaseSearchTree method)

alpha (PhaseResult attribute) angles (XRDData property) angular_correction() (in module dara.utils) atom_positions_string (PhaseResult attribute)

B

b (PhaseResult attribute) BaseSearchTree (class in dara.search.tree) batch_peak_matching() (in module dara.search.tree) batch_refinement() (in module dara.search.tree) best_rwp (PhaseSearchDocument attribute)

beta (PhaseResult attribute) BGMNWorker (class in dara.bgmn_worker) binary_data (RASXFile property) (RawFile property) bool2yn() (in module dara.utils)

C

c (PhaseResult attribute) calculate_fom_and_strain() (in module dara.search.tree) CellularAutomatonEngine (class in dara.prediction.rxn_ca) check_gewicht() (PhaseResult class method) check_wyckoff() (in module dara.cif2str) Cif (class in dara.cif) cif2str() (in module dara.cif2str) CIF2StrError CifBlock (class in dara.cif) cifs_folder_name (PhaseSearchDocument attribute) (PhaseSearchMaker attribute)

cli_cmd() (DaraCli method) (Server method) CODDatabase (class in dara.structure_db) compositions_to_array() (in module dara.utils) CONFIG_FILE (DaraSettings attribute) convert_to_local_tz() (in module dara.server.utils) copy_and_rename_files() (in module dara.utils) copy_instrument_files() (in module dara.generate_control_file) copy_xy_pattern() (in module dara.generate_control_file) current_phases (SearchNodeData attribute) current_result (SearchNodeData attribute)

D

d (LstResult attribute) dara module dara.bgmn module dara.bgmn.download_bgmn module dara.bgmn_worker module dara.cif module dara.cif2str module dara.cli module dara.data module dara.eflech_worker module dara.generate_control_file module dara.jobs module dara.peak_detection module dara.plot module dara.prediction module dara.prediction.base module dara.prediction.core module dara.prediction.rn module dara.prediction.rxn_ca module dara.refine module dara.result module dara.schema module

dara.search module dara.search.core module dara.search.data_model module dara.search.peak_matcher module dara.search.tree module dara.server module dara.server.api_router module dara.server.app module dara.server.setting module dara.server.utils module dara.server.worker module dara.settings module dara.structure_db module dara.utils module dara.xrd module database_backend (DaraServerSettings attribute), [1] datetime_str() (in module dara.utils) default_folder_path (CODDatabase property) (ICSDDatabase property) (StructureDatabase property) detect_peaks() (in module dara.peak_detection) distance_matrix() (in module dara.search.peak_matcher) do_refinement() (in module dara.refine) do_refinement_no_saving() (in module dara.refine) download_bgmn() (in module dara.bgmn.download_bgmn) download_structures() (CODDatabase method) (ICSDDatabase method) (StructureDatabase method)

E

EflechWorker (class in dara.eflech_worker) errors (XRDData property) expand_node() (BaseSearchTree method) expand_root() (BaseSearchTree method)

export_structure() (RefinementResult method) extra (PeakMatcher property) extra_peaks (PhaseSearchDocument attribute) (SearchResult attribute)

F

final_refinement_params (PhaseSearchDocument attribute) final_result (PhaseSearchDocument attribute) find_best_match() (in module dara.search.peak_matcher) find_optimal_intensity_threshold() (in module dara.utils) find_optimal_score_threshold() (in module dara.utils) fom (SearchNodeData attribute) foms (PhaseSearchDocument attribute) (SearchResult attribute) from_file() (Cif class method) (RASXFile class method) (RawFile class method) (XRDData class method) (XRDMLFile class method) (XYFile class method)

from_search_tree() (BaseSearchTree class method) from_str() (Cif class method) from_structure() (Cif class method) fuzzy_compare() (in module dara.utils)

G

gamma (PhaseResult attribute) generate_control_file() (EflechWorker static method) (in module dara.generate_control_file) get_all_pending_jobs() (in module dara.server.worker) get_all_possible_nodes_at_same_level() (BaseSearchTree method) get_all_tasks() (in module dara.server.api_router) get_background_breakpoints() (EflechWorker static method) get_chemsys_from_formulas() (in module dara.utils) get_cifs_by_chemsys() (StructureDatabase method) get_cifs_by_formulas() (StructureDatabase method) get_composition_distance() (in module dara.utils) get_composition_from_filename() (in module dara.utils) get_compositional_clusters() (in module dara.utils) get_dara_server_settings() (in module dara.server.setting) get_disordered_cifs() (Cif method) get_disordered_structures() (Cif method) get_entries_db() (in module dara.utils) get_entries_in_chemsys_db() (in module dara.utils) get_entries_in_chemsys_mp() (in module dara.utils) get_entry_by_formula() (in module dara.prediction.rn) get_expandable_children() (BaseSearchTree method) get_file_path() (CODDatabase method) (ICSDDatabase method) (StructureDatabase method) get_formula_data() (StructureDatabase method) get_formula_with_disorder() (in module dara.cif)

get_head_of_compositional_cluster() (in module dara.utils) get_isolated_peaks() (PeakMatcher method) get_job_store() (in module dara.server.utils) get_lattice_parameters_from_lattice() (in module dara.cif2str) get_logger() (in module dara.utils) get_natural_break_results() (in module dara.search.tree) get_number() (in module dara.utils) get_optimal_max_two_theta() (in module dara.utils) get_peak_matcher() (SearchNodeData method) get_phase_combinations() (BaseSearchTree method) get_phase_weights() (RefinementResult method) get_result() (in module dara.result) get_result_store() (in module dara.server.utils) get_search_results() (SearchTree method) get_std_position() (in module dara.cif2str) get_store() (in module dara.server.utils) get_structure() (PhaseResult method) get_wavelength() (in module dara.utils) get_worker_store() (in module dara.server.utils) get_xrdml_data() (in module dara.xrd) gewicht (PhaseResult attribute) gewicht_name (PhaseResult attribute) group_id (SearchNodeData attribute) group_phases() (in module dara.search.tree) grouped_phases (PhaseSearchDocument attribute) (SearchResult property)

H

hermann_mauguin (PhaseResult attribute) hex2float() (in module dara.xrd)

hex2int() (in module dara.xrd) host (DaraServerSettings attribute), [1]

I

ICSDDatabase (class in dara.structure_db) input_cifs (PhaseSearchDocument attribute) instrument_name (RefinementDocument attribute)

intensities (XRDData property) intensity_correction() (in module dara.utils) isolated_extra_peaks (SearchNodeData attribute) isolated_missing_peaks (SearchNodeData attribute)

J

jaccard_index() (PeakMatcher method)

L

last_updated (PhaseSearchDocument attribute) (RefinementDocument attribute) lattice_strain (SearchNodeData attribute) lattice_strains (PhaseSearchDocument attribute) (SearchResult attribute) launch_app() (in module dara.server.app) launch_worker_process() (in module dara.server.app)

load_default_settings() (DaraSettings class method) load_rasx() (in module dara.xrd) load_raw() (in module dara.xrd) load_symmetrized_structure() (in module dara.utils) load_xrdml() (in module dara.xrd) local_copy_found (StructureDatabase property) lst_data (RefinementResult attribute)

M

main() (in module dara.cli) make() (PhaseSearchMaker method) (RefinementMaker method) (RefinementPhase class method) make_lattice_parameters_str() (in module dara.cif2str) make_peak_parameter_str() (in module dara.cif2str) make_spacegroup_setting_str() (in module dara.cif2str) mark_running_jobs_as_fizzled() (in module dara.server.worker) matched (PeakMatcher property) max_num_results (PhaseSearchMaker attribute) merge_peaks() (in module dara.search.peak_matcher) missing (PeakMatcher property) missing_peaks (PhaseSearchDocument attribute) (SearchResult attribute) module dara dara.bgmn dara.bgmn.download_bgmn dara.bgmn_worker dara.cif dara.cif2str dara.cli dara.data dara.eflech_worker dara.generate_control_file dara.jobs dara.peak_detection dara.plot dara.prediction dara.prediction.base dara.prediction.core dara.prediction.rn dara.prediction.rxn_ca dara.refine dara.result dara.schema dara.search dara.search.core dara.search.data_model dara.search.peak_matcher dara.search.tree dara.server dara.server.api_router dara.server.app dara.server.setting dara.server.utils dara.server.worker dara.settings dara.structure_db dara.utils dara.xrd

mongodb_database (DaraServerSettings attribute), [1] mongodb_host (DaraServerSettings attribute), [1] mongodb_password (DaraServerSettings attribute), [1] mongodb_port (DaraServerSettings attribute), [1] mongodb_username (DaraServerSettings attribute), [1] montydb_path (DaraServerSettings attribute), [1]

N

name (Cif property) (CODDatabase property) (ICSDDatabase property) (PhaseSearchMaker attribute) (RefinementMaker attribute) (StructureDatabase property)

num_steps (LstResult attribute)

P

params (RefinementPhase attribute) parse_dia() (in module dara.result) parse_lst() (in module dara.result) parse_par() (in module dara.result) parse_par_file() (EflechWorker static method) parse_peak_list() (EflechWorker method) parse_refinement_param() (in module dara.utils) ParseError patch_control_file_after_teil() (EflechWorker method) path (RefinementPhase attribute) (StructureDatabase property) PATH_TO_COD (DaraSettings attribute) PATH_TO_ICSD (DaraSettings attribute) pattern_name (LstResult attribute) peak_data (RefinementResult attribute) peak_matcher_scores (SearchNodeData attribute) peak_matcher_threshold (SearchNodeData attribute) PeakMatcher (class in dara.search.peak_matcher) phase_params (RefinementDocument attribute) phase_predictor (PhaseSearchDocument attribute) (PhaseSearchMaker attribute)

PhasePredictor (class in dara.prediction.core) phases (SearchResult attribute) phases_results (LstResult attribute) PhaseSearchMaker (class in dara.jobs) plot() (in module dara.server.api_router) (XRDData method) plot_data (RefinementResult attribute) port (DaraServerSettings attribute), [1] precursors (PhaseSearchDocument attribute) predict() (CellularAutomatonEngine method) (PhasePredictor method) (PredictionEngine method) (ReactionNetworkEngine method) predict_kwargs (PhaseSearchDocument attribute) PredictionEngine (class in dara.prediction.base) preparsed_info (StructureDatabase property) pretty_output (SearchNodeData property) process_phase_name() (in module dara.utils) process_specie_string() (in module dara.cif2str)

R

r (LstResult attribute) rasx2xy() (in module dara.xrd) RASXFile (class in dara.xrd) raw2xy() (in module dara.xrd) raw_lst (LstResult attribute) RawFile (class in dara.xrd) ReactionNetworkEngine (class in dara.prediction.rn) read_phase_name_from_str() (in module dara.utils) refine_phases() (BaseSearchTree method) refinement_params (RefinementDocument attribute) (RefinementMaker attribute) refinement_result (SearchResult attribute) RefinementMaker (class in dara.jobs) remote_expand_node() (in module dara.search.core) remove_unnecessary_phases() (in module dara.search.tree) result (RefinementDocument attribute)

result() (in module dara.server.api_router) results (PhaseSearchDocument attribute) rexp (LstResult attribute) rho (LstResult attribute) rp (LstResult attribute) rpb (LstResult attribute) rpb() (in module dara.utils) rphase (PhaseResult attribute) run_eflech() (EflechWorker method) run_final_refinement (PhaseSearchDocument attribute) (PhaseSearchMaker attribute) run_job() (in module dara.server.worker) run_peak_detection() (EflechWorker method) run_refinement_cmd() (BGMNWorker method) rwp (LstResult attribute) (RefinementDocument attribute) rwp() (in module dara.utils)

S

save (RefinementMaker attribute) score() (PeakMatcher method) score_phases() (BaseSearchTree method) search_kwargs (PhaseSearchDocument attribute) search_phases() (in module dara.search.core) SearchTree (class in dara.search.tree) server (DaraCli attribute)

show() (SearchTree method) show_progress (RefinementMaker attribute) spacegroup_no (PhaseResult attribute) standardize_coords() (in module dara.utils) status (SearchNodeData attribute) structs (DiaResult attribute) StructureDatabase (class in dara.structure_db) submit() (in module dara.server.api_router)

T

task_label (PhaseSearchDocument attribute) (RefinementDocument attribute) to_file() (Cif method) to_rasx_file() (RASXFile method) to_raw_file() (RawFile method)

to_scaled_structure() (Cif method) to_structure() (Cif method) to_xrdml_file() (XRDMLFile method) to_xy_file() (XRDData method) transform() (RefinementResult class method) trim_pattern() (in module dara.generate_control_file)

U

unit (PhaseResult attribute)

V

verbose (PhaseSearchMaker attribute) visualize() (in module dara.plot) (PeakMatcher method) (RefinementResult method) (SearchResult method)

W

worker_process() (in module dara.server.worker)

write_cifs_from_formulas() (PhasePredictor method) wrong_intensity (PeakMatcher property)

X

x (DiaResult attribute) xray_density (PhaseResult attribute) xrd_data (PhaseSearchDocument attribute) (RefinementDocument attribute)

XRDData (class in dara.xrd) xrdml2xy() (in module dara.xrd) xrdml_dict (XRDMLFile property) XRDMLFile (class in dara.xrd) XYFile (class in dara.xrd)

Y

y_bkg (DiaResult attribute)

y_calc (DiaResult attribute) y_obs (DiaResult attribute)