Index

_

__init__() (modifinder.classes.Compound method) (modifinder.classes.Spectrum method)

A

accession_to_usi() (in module modifinder.utilities.network) add_adduct_to_formula() (in module modifinder.utilities.general_utils) add_adjusted_edge() (modifinder.classes.ModiFinder.ModiFinder method) add_neighbor() (modifinder.classes.ModiFinder.ModiFinder method) align() (modifinder.engines.Abtracts.AlignmentEngine method) (modifinder.engines.alignment.CosineAlignmentEngine.CosineAlignmentEngine method) align_single() (modifinder.engines.Abtracts.AlignmentEngine method) (modifinder.engines.alignment.CosineAlignmentEngine.CosineAlignmentEngine method)

AlignmentEngine (class in modifinder.engines.Abtracts) annotate() (modifinder.engines.Abtracts.AnnotationEngine method) (modifinder.engines.annotation.MAGMaAnnotationEngine.MAGMaAnnotationEngine method) annotate_single() (modifinder.engines.Abtracts.AnnotationEngine method) (modifinder.engines.annotation.MAGMaAnnotationEngine.MAGMaAnnotationEngine method) AnnotationEngine (class in modifinder.engines.Abtracts) attach_mols() (in module modifinder.utilities.mol_utils)

B

BasicEvaluationEngine (class in modifinder.engines.evaluation)

C

calculate_annotation_entropy() (modifinder.Compound method) calculate_contribution_atom_in_peak() (modifinder.Compound method) calculate_contributions() (modifinder.Compound method) calculate_peak_annotation_ambiguity() (modifinder.Compound method) clear() (modifinder.Compound method) (modifinder.Spectrum method) Compound (class in modifinder.classes)

compound_to_dict() (in module modifinder.convert) convert_to_formula() (in module modifinder.utilities.general_utils) convert_to_universal_key() (in module modifinder.utilities.general_utils) copy() (modifinder.classes.EdgeDetail.EdgeDetail method) (modifinder.classes.EdgeDetail.Match method) (modifinder.Compound method) CosineAlignmentEngine (class in modifinder.engines.alignment.CosineAlignmentEngine)

D

draw_alignment() (in module modifinder.utilities.visualizer) (modifinder.classes.ModiFinder.ModiFinder method) draw_frag_of_molecule() (in module modifinder.utilities.visualizer) draw_modifications() (in module modifinder.utilities.visualizer)

draw_molecule() (in module modifinder.utilities.visualizer) draw_molecule_heatmap() (in module modifinder.utilities.visualizer) draw_prediction() (modifinder.classes.ModiFinder.ModiFinder method) draw_spectrum() (in module modifinder.utilities.visualizer)

E

EdgeDetail (class in modifinder.classes.EdgeDetail) entropy() (in module modifinder.utilities.general_utils) evaluate() (modifinder.engines.Abtracts.EvaluationEngine method) (modifinder.engines.evaluation.BasicEvaluationEngine method)

evaluate_single() (modifinder.engines.Abtracts.EvaluationEngine method) (modifinder.engines.evaluation.BasicEvaluationEngine method) EvaluationEngine (class in modifinder.engines.Abtracts)

F

filter_fragments_by_atoms() (modifinder.Compound method)

find_existance() (modifinder.Compound method)

G

generate_possible_stuctures() (in module modifinder.utilities.mol_utils) generate_probabilities() (modifinder.classes.ModiFinder.ModiFinder method) get_adduct_mass() (in module modifinder.utilities.general_utils) get_data() (in module modifinder.utilities.network) get_diff() (in module modifinder.utilities.general_utils) get_edge_detail() (modifinder.classes.ModiFinder.ModiFinder method) get_edit_distance() (in module modifinder.utilities.mol_utils) get_edit_distance_detailed() (in module modifinder.utilities.mol_utils) get_elements() (in module modifinder.utilities.general_utils)

get_formula_mass() (in module modifinder.utilities.general_utils) get_fragment_info() (modifinder.engines.Abtracts.AnnotationEngine method) (modifinder.engines.annotation.MAGMaAnnotationEngine.MAGMaAnnotationEngine method) get_matched_peaks() (in module modifinder.utilities.network) get_matches_pairs() (modifinder.classes.EdgeDetail.EdgeDetail method) get_meta_data() (modifinder.Compound method) get_modification_edges() (in module modifinder.utilities.mol_utils) get_modification_graph() (in module modifinder.utilities.mol_utils) get_modification_nodes() (in module modifinder.utilities.mol_utils) get_transition() (in module modifinder.utilities.mol_utils)

I

intensity (modifinder.utilities.gnps_types.SpectrumTuple attribute)

is_shifted() (in module modifinder.utilities.general_utils) is_submolecule() (in module modifinder.utilities.general_utils)

K

keep_top_k() (modifinder.Spectrum method)

M

MAGMaAnnotationEngine (class in modifinder.engines.annotation.MAGMaAnnotationEngine) Match (class in modifinder.classes.EdgeDetail) MatchType (class in modifinder.classes.EdgeDetail) ModiFinder (class in modifinder.classes.ModiFinder) modifinder.classes.EdgeDetail module modifinder.classes.ModiFinder module modifinder.convert module modifinder.engines.Abtracts module modifinder.engines.alignment.CosineAlignmentEngine module modifinder.engines.annotation.MAGMaAnnotationEngine module modifinder.utilities.general_utils module modifinder.utilities.gnps_types module

modifinder.utilities.mol_utils module modifinder.utilities.network module modifinder.utilities.visualizer module module modifinder.classes.EdgeDetail modifinder.classes.ModiFinder modifinder.convert modifinder.engines.Abtracts modifinder.engines.alignment.CosineAlignmentEngine modifinder.engines.annotation.MAGMaAnnotationEngine modifinder.utilities.general_utils modifinder.utilities.gnps_types modifinder.utilities.mol_utils modifinder.utilities.network modifinder.utilities.visualizer mz (modifinder.utilities.gnps_types.SpectrumTuple attribute)

N

normalize_peaks() (modifinder.Spectrum method)

P

parse_data_to_universal() (in module modifinder.utilities.general_utils) parse_molecular_formula() (in module modifinder.utilities.general_utils) power_prob() (in module modifinder.utilities.general_utils)

precursor_charge (modifinder.utilities.gnps_types.SpectrumTuple attribute) precursor_mz (modifinder.utilities.gnps_types.SpectrumTuple attribute) print_peaks_to_fragments_map() (modifinder.Compound method)

R

re_align() (modifinder.classes.ModiFinder.ModiFinder method) re_annotate() (modifinder.classes.ModiFinder.ModiFinder method) read_mgf() (in module modifinder.utilities.general_utils) refine_annotations_by_formula() (modifinder.engines.annotation.MAGMaAnnotationEngine.MAGMaAnnotationEngine method)

refine_annotations_by_helper() (modifinder.engines.annotation.MAGMaAnnotationEngine.MAGMaAnnotationEngine method) remove_adduct_from_formula() (in module modifinder.utilities.general_utils) remove_small_peaks() (modifinder.Spectrum method) return_public_functions() (in module modifinder.utilities.visualizer) reverse_match() (modifinder.classes.EdgeDetail.EdgeDetail method)

S

shifted (modifinder.classes.EdgeDetail.MatchType attribute) solve() (modifinder.classes.ModiFinder.ModiFinder method)

Spectrum (class in modifinder.classes) spectrum_to_dict() (in module modifinder.convert) SpectrumTuple (class in modifinder.utilities.gnps_types)

T

to_compound() (in module modifinder.convert)

to_spectrum() (in module modifinder.convert)

U

unshifted (modifinder.classes.EdgeDetail.MatchType attribute) update() (modifinder.Compound method) (modifinder.Spectrum method)

update_edge() (modifinder.classes.ModiFinder.ModiFinder method) usi_to_accession() (in module modifinder.utilities.network)

W

write_mgf() (in module modifinder.utilities.general_utils)