Index

_

__init__() (simba.core.data.spectrum.SpectrumExt method) (simba.core.models.transformers.CustomDatasetEncoder.CustomDatasetEncoder method) (simba.core.models.transformers.CustomDatasetMultitasking.CustomDatasetMultitasking method) (simba.core.models.transformers.CustomDatasetUnique.CustomDatasetUnique method) (simba.core.models.transformers.embedder.Embedder method) (simba.core.models.transformers.spectrum_transformer_encoder_custom.SpectrumTransformerEncoderCustom method)

A

add_high_similarity_pairs_edit_distance() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method) adduct_mass_map (simba.core.models.transformers.spectrum_transformer_encoder_custom.SpectrumTransformerEncoderCustom attribute)

AnalogDiscovery (class in simba.analog_discovery.simba_analog_discovery) are_weights_changed() (simba.core.models.transformers.embedder.Embedder method) attach_mols() (in module simba.core.chemistry.edit_distance.mol_utils)

C

categorical_adduct (simba.core.models.transformers.spectrum_transformer_encoder_custom.SpectrumTransformerEncoderCustom attribute) compute_all_combinations() (simba.analog_discovery.fc_layers_analog_discovery.FcLayerAnalogDiscovery static method) compute_ed_or_mces() (in module simba.core.chemistry.edit_distance.edit_distance) compute_edit_distance() (simba.core.data.ground_truth.GroundTruth method) compute_emb_from_existing_embeddings() (simba.analog_discovery.fc_layers_analog_discovery.FcLayerAnalogDiscovery static method) compute_mces() (simba.core.data.ground_truth.GroundTruth method) compute_ranking() (simba.analog_discovery.simba_analog_discovery.AnalogDiscovery static method)

compute_tanimoto() (simba.core.data.ground_truth.GroundTruth method) configure_optimizers() (simba.core.models.transformers.embedder.Embedder method) create_input_df() (in module simba.core.chemistry.edit_distance.edit_distance) custom_random() (simba.core.models.ordinal.ordinal_classification.OrdinalClassification static method) CustomDatasetEncoder (class in simba.core.models.transformers.CustomDatasetEncoder) CustomDatasetMultitasking (class in simba.core.models.transformers.CustomDatasetMultitasking) CustomDatasetUnique (class in simba.core.models.transformers.CustomDatasetUnique)

D

default_filters() (simba.core.data.loaders.LoadData static method)

E

Embedder (class in simba.core.models.transformers.embedder)

F

FcLayerAnalogDiscovery (class in simba.analog_discovery.fc_layers_analog_discovery) find_file() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method)

forward() (simba.core.models.transformers.embedder.Embedder method) from_float_to_class() (simba.core.models.ordinal.ordinal_classification.OrdinalClassification static method)

G

generate_possible_stuctures() (in module simba.core.chemistry.edit_distance.mol_utils) get_all_keys() (simba.core.models.transformers.embedder.Embedder method) get_all_spectra() (simba.core.data.loaders.LoadData method) get_all_spectra_casmi() (simba.core.data.loaders.LoadData method) get_all_spectra_mgf() (simba.core.data.loaders.LoadData method) get_all_spectra_nist() (simba.core.data.loaders.LoadData method) get_class() (simba.core.data.preprocessing.PreprocessingUtils method) get_data() (in module simba.core.chemistry.edit_distance.edit_distance) get_edit_distance() (in module simba.core.chemistry.edit_distance.mol_utils) get_edit_distance_detailed() (in module simba.core.chemistry.edit_distance.mol_utils) get_edit_distance_from_smiles() (in module simba.core.chemistry.edit_distance.edit_distance)

get_maldi_embedder_keys() (simba.core.models.transformers.embedder.Embedder method) get_modification_edges() (in module simba.core.chemistry.edit_distance.mol_utils) get_modification_graph() (in module simba.core.chemistry.edit_distance.mol_utils) get_modification_nodes() (in module simba.core.chemistry.edit_distance.mol_utils) get_number_of_modification_edges() (in module simba.core.chemistry.edit_distance.edit_distance) get_original_dictionary() (simba.core.models.transformers.CustomDatasetMultitasking.CustomDatasetMultitasking method) (simba.core.models.transformers.CustomDatasetUnique.CustomDatasetUnique method) get_precursor_mz() (simba.core.data.loaders.LoadData static method) get_spectra() (simba.core.data.loaders.LoadData method) get_transition() (in module simba.core.chemistry.edit_distance.mol_utils) GroundTruth (class in simba.core.data.ground_truth)

I

is_centroid() (simba.core.data.preprocessing.PreprocessingUtils static method)

is_valid_spectrum_gnps() (simba.core.data.loaders.LoadData static method) is_valid_spectrum_janssen() (simba.core.data.loaders.LoadData static method)

L

load_full_model() (simba.analog_discovery.fc_layers_analog_discovery.FcLayerAnalogDiscovery static method) load_mces_20_data() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method) load_pretrained_maldi_embedder() (simba.core.models.transformers.embedder.Embedder method) load_raw_data() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method)

load_spectra() (simba.core.data.preprocessing_simba.PreprocessingSimba method) load_weights() (simba.core.models.transformers.embedder.Embedder method) LoadData (class in simba.core.data.loaders) LoadMCES (class in simba.core.chemistry.mces_loader.load_mces)

M

merge_numpy_arrays() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method) merge_numpy_arrays_edit_distance() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method) merge_numpy_arrays_mces() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method) merge_numpy_arrays_multitask() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method) module simba.analog_discovery.fc_layers_analog_discovery simba.analog_discovery.simba_analog_discovery simba.core.chemistry.edit_distance.edit_distance simba.core.chemistry.edit_distance.mol_utils simba.core.chemistry.mces_loader.load_mces simba.core.data.ground_truth simba.core.data.loaders simba.core.data.preprocessing simba.core.data.preprocessing_simba simba.core.data.spectrum simba.core.models.ordinal.ordinal_classification

N

normalize_ed() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method)

normalize_mces20() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method) normalized_dot_product() (simba.core.models.transformers.embedder.Embedder method)

O

order_by_charge() (simba.core.data.preprocessing.PreprocessingUtils static method)

order_spectra_by_mz() (simba.core.data.preprocessing.PreprocessingUtils static method) OrdinalClassification (class in simba.core.models.ordinal.ordinal_classification)

P

precursor_hook() (simba.core.models.transformers.spectrum_transformer_encoder_custom.SpectrumTransformerEncoderCustom method) predict_step() (simba.core.models.transformers.embedder.Embedder method)

PreprocessingSimba (class in simba.core.data.preprocessing_simba) PreprocessingUtils (class in simba.core.data.preprocessing)

R

remove_excess_low_pairs() (simba.core.chemistry.mces_loader.load_mces.LoadMCES static method)

return_mol() (in module simba.core.chemistry.edit_distance.edit_distance)

S

set_freeze_layers() (simba.core.models.transformers.embedder.Embedder method) set_max_peak() (simba.core.data.spectrum.SpectrumExt method) set_murcko_scaffold() (simba.core.data.spectrum.SpectrumExt method) set_params() (simba.core.data.spectrum.SpectrumExt method) set_smiles() (simba.core.data.spectrum.SpectrumExt method) set_spectrum_vector() (simba.core.data.spectrum.SpectrumExt method) simba.analog_discovery.fc_layers_analog_discovery module simba.analog_discovery.simba_analog_discovery module simba.core.chemistry.edit_distance.edit_distance module simba.core.chemistry.edit_distance.mol_utils module simba.core.chemistry.mces_loader.load_mces module simba.core.data.ground_truth module

simba.core.data.loaders module simba.core.data.preprocessing module simba.core.data.preprocessing_simba module simba.core.data.spectrum module simba.core.models.ordinal.ordinal_classification module simba_get_edit_distance() (in module simba.core.chemistry.edit_distance.edit_distance) simba_solve_pair_edit_distance() (in module simba.core.chemistry.edit_distance.edit_distance) simba_solve_pair_mces() (in module simba.core.chemistry.edit_distance.edit_distance) SpectrumExt (class in simba.core.data.spectrum) SpectrumTransformerEncoderCustom (class in simba.core.models.transformers.spectrum_transformer_encoder_custom) step() (simba.core.models.transformers.embedder.Embedder method)

T

training_step() (simba.core.models.transformers.embedder.Embedder method)

U

use_adduct (simba.core.models.transformers.spectrum_transformer_encoder_custom.SpectrumTransformerEncoderCustom attribute) use_ce (simba.core.models.transformers.spectrum_transformer_encoder_custom.SpectrumTransformerEncoderCustom attribute)

use_ion_activation (simba.core.models.transformers.spectrum_transformer_encoder_custom.SpectrumTransformerEncoderCustom attribute) use_ion_method (simba.core.models.transformers.spectrum_transformer_encoder_custom.SpectrumTransformerEncoderCustom attribute)

V

validation_step() (simba.core.models.transformers.embedder.Embedder method)