Index

_

__eq__() (DecisionTreeVisualiser method) __getstate__() (DecisionTreeVisualiser method) __ne__() (DecisionTreeVisualiser method)

__repr__() (DecisionTreeVisualiser method) (PredictionResult method) __setattr__() (DecisionTreeVisualiser method) __setstate__() (DecisionTreeVisualiser method)

A

align_and_filter_peaks() (in module gunshotmatch_pipeline.peaks)

C

class_name (namedtuple field) PredictionResult (namedtuple in gunshotmatch_pipeline.decision_tree.predictions) classifier (DecisionTreeVisualiser attribute) compounds() (in module gunshotmatch_pipeline.results) compounds_from_matches() (in module gunshotmatch_pipeline.results)

config (GlobalSettings attribute) (ProjectSettings attribute) (UnknownSettings attribute) Configuration (class in gunshotmatch_pipeline.config) correct() (PredictionResult property)

D

data_directory (GlobalSettings attribute) (ProjectSettings attribute) (UnknownSettings attribute) data_from_projects() (in module gunshotmatch_pipeline.decision_tree) data_from_unknown() (in module gunshotmatch_pipeline.decision_tree) datafile (UnknownSettings attribute) datafile_path() (UnknownSettings property)

datafiles (ProjectSettings attribute) DecisionTreeVisualiser (class in gunshotmatch_pipeline.decision_tree) deinit() (LazyEngine method) deserialise_decision_tree() (in module gunshotmatch_pipeline.decision_tree.export) deserialise_random_forest() (in module gunshotmatch_pipeline.decision_tree.export) dotsafe_name() (in module gunshotmatch_pipeline.decision_tree) dump_predictions() (in module gunshotmatch_pipeline.decision_tree.predictions)

E

engine() (LazyEngine property)

engine_on_demand() (in module gunshotmatch_pipeline.nist_ms_search)

F

factorize_map (DecisionTreeVisualiser attribute) feature_names (DecisionTreeVisualiser attribute) filter_and_identify_peaks() (in module gunshotmatch_pipeline.unknowns) fit_decision_tree() (in module gunshotmatch_pipeline.decision_tree) friendly_name_mapping (in module gunshotmatch_pipeline.utils) from_data() (DecisionTreeVisualiser class method)

from_json() (Configuration class method) (Projects class method) (UnknownSettings class method) from_toml() (Configuration class method) (Projects class method) (UnknownSettings class method)

G

get_datafile_paths() (ProjectSettings method) get_feature_names() (in module gunshotmatch_pipeline.decision_tree) get_project_settings() (Projects method) global_settings (Projects attribute) GlobalSettings (class in gunshotmatch_pipeline.projects) gunshotmatch_pipeline module gunshotmatch_pipeline.config module gunshotmatch_pipeline.decision_tree module gunshotmatch_pipeline.decision_tree.export module gunshotmatch_pipeline.decision_tree.predictions module

gunshotmatch_pipeline.exporters module gunshotmatch_pipeline.nist_ms_search module gunshotmatch_pipeline.peaks module gunshotmatch_pipeline.projects module gunshotmatch_pipeline.results module gunshotmatch_pipeline.unknowns module gunshotmatch_pipeline.utils module

H

has_common_config() (Projects method)

has_common_method() (Projects method)

I

iter_loaded_projects() (Projects method)

iter_project_settings() (Projects method)

L

LazyEngine (class in gunshotmatch_pipeline.nist_ms_search) library_path (PyMSNISTSearchCfg attribute) load_config() (LoaderMixin method)

load_method() (LoaderMixin method) load_predictions() (in module gunshotmatch_pipeline.decision_tree.predictions) load_project() (Projects method) LoaderMixin (class in gunshotmatch_pipeline.projects)

M

machine_learning_data() (in module gunshotmatch_pipeline.results) Matches (typeddict in gunshotmatch_pipeline.results) matches() (in module gunshotmatch_pipeline.results) MatchesCompounds (typeddict in gunshotmatch_pipeline.results) MatchesMetadata (typeddict in gunshotmatch_pipeline.results) method (GlobalSettings attribute) (ProjectSettings attribute) (UnknownSettings attribute) MIT License, [1] module gunshotmatch_pipeline gunshotmatch_pipeline.config gunshotmatch_pipeline.decision_tree gunshotmatch_pipeline.decision_tree.export gunshotmatch_pipeline.decision_tree.predictions gunshotmatch_pipeline.exporters gunshotmatch_pipeline.nist_ms_search gunshotmatch_pipeline.peaks gunshotmatch_pipeline.projects gunshotmatch_pipeline.results gunshotmatch_pipeline.unknowns gunshotmatch_pipeline.utils

N

name (namedtuple field) PredictionResult (namedtuple in gunshotmatch_pipeline.decision_tree.predictions) name (ProjectSettings attribute) (UnknownSettings attribute)

NameMapping (class in gunshotmatch_pipeline.utils) nist_ms_search_engine() (in module gunshotmatch_pipeline.nist_ms_search)

O

output_directory (GlobalSettings attribute) (UnknownSettings attribute)

P

predictions (namedtuple field) PredictionResult (namedtuple in gunshotmatch_pipeline.decision_tree.predictions) per_project_settings (Projects attribute) predict_unknown() (in module gunshotmatch_pipeline.decision_tree) PredictionResult (namedtuple in gunshotmatch_pipeline.decision_tree.predictions) class_name (namedtuple field) name (namedtuple field) predictions (namedtuple field) prepare_datafile() (in module gunshotmatch_pipeline) prepare_peak_list() (in module gunshotmatch_pipeline.peaks)

process_projects() (in module gunshotmatch_pipeline.projects) process_unknown() (in module gunshotmatch_pipeline.unknowns) project_from_repeats() (in module gunshotmatch_pipeline) project_plural (in module gunshotmatch_pipeline.utils) Projects (class in gunshotmatch_pipeline.projects) ProjectSettings (class in gunshotmatch_pipeline.projects) pyms_nist_search (Configuration attribute) PyMSNISTSearchCfg (class in gunshotmatch_pipeline.nist_ms_search) Python Enhancement Proposals PEP 517

S

serialise_decision_tree() (in module gunshotmatch_pipeline.decision_tree.export)

serialise_random_forest() (in module gunshotmatch_pipeline.decision_tree.export) simulate_data() (in module gunshotmatch_pipeline.decision_tree)

T

to_toml() (Configuration method) (Projects method) (UnknownSettings method)

U

unknown() (in module gunshotmatch_pipeline.results) unknown_machine_learning_data() (in module gunshotmatch_pipeline.results)

unknown_plural (in module gunshotmatch_pipeline.utils) UnknownSettings (class in gunshotmatch_pipeline.unknowns) user_library (PyMSNISTSearchCfg attribute)

V

verify_saved_datafile() (in module gunshotmatch_pipeline.exporters) verify_saved_decision_tree() (in module gunshotmatch_pipeline.decision_tree.export) verify_saved_project() (in module gunshotmatch_pipeline.exporters)

verify_saved_random_forest() (in module gunshotmatch_pipeline.decision_tree.export) visualise_decision_tree() (in module gunshotmatch_pipeline.decision_tree) visualise_tree() (DecisionTreeVisualiser method)

W

write_combined_csv() (in module gunshotmatch_pipeline.exporters)

write_matches_json() (in module gunshotmatch_pipeline.exporters)