Index

_

__call__() (dreams.utils.data.SpectrumPreprocessor method)

__getitem__() (dreams.utils.data.MaskedSpectraDataset method) __len__() (dreams.utils.data.MaskedSpectraDataset method)

A

acc_est_weight (dreams.utils.data.MaskedSpectraDataset attribute) add_column() (dreams.utils.data.MSData method) all_close_pairwise() (in module dreams.utils.misc) allow_zero_length_dataloader_with_multiple_devices (dreams.utils.data.CVDataModule attribute) (dreams.utils.data.RandomSplitDataModule attribute) (dreams.utils.data.SplittedDataModule attribute) AnnotatedSpectraDataset (class in dreams.utils.data)

append_to_stem() (in module dreams.utils.io) are_sub_hists() (in module dreams.algorithms.murcko_hist) (in module dreams.algorithms.murcko_hist.murcko_hist) assign_colors() (in module dreams.utils.plots) assign_dformat() (in module dreams.utils.dformats) at() (dreams.utils.data.MSData method) AttentionEntropyValidation (class in dreams.utils.data) available_models() (dreams.api.PreTrainedModel static method)

B

backbone (dreams.models.heads.heads.FineTuningHead attribute) BatchedPeakListRandomProjection (class in dreams.algorithms.lsh) (class in dreams.algorithms.lsh.lsh) bert801010_masking (dreams.utils.data.MaskedSpectraDataset attribute) bin_peak_list() (in module dreams.utils.spectra)

bin_peak_lists() (in module dreams.utils.spectra) BinClassificationHead (class in dreams.models.heads.heads) break_rings() (in module dreams.algorithms.murcko_hist.murcko_hist) buf (dreams.utils.io.TqdmToLogger attribute) bytes_to_human_str() (in module dreams.utils.io) bytes_to_units() (in module dreams.utils.io)

C

cache_pkl() (in module dreams.utils.io) calc_attention_entropy() (in module dreams.utils.misc) CENTROID (dreams.utils.lcms.SpecType attribute) chunk_list() (in module dreams.utils.misc) chunk_list_eq_sum() (in module dreams.utils.misc) ChunkedDatasetAccessor (class in dreams.utils.io) ChunkedHDF5File (class in dreams.utils.io) clean_ftps() (in module dreams.utils.io) close() (dreams.utils.io.ChunkedHDF5File method) closest_mz_frags() (in module dreams.utils.mols) color_generator() (in module dreams.utils.plots) columns() (dreams.utils.data.MSData method) complete_permutation() (in module dreams.utils.misc) compress_hdf() (in module dreams.utils.io) compute() (dreams.algorithms.lsh.BatchedPeakListRandomProjection method) (dreams.algorithms.lsh.lsh.BatchedPeakListRandomProjection method) (dreams.algorithms.lsh.lsh.PeakListRandomProjection method) (dreams.algorithms.lsh.lsh.RandomProjection method) (dreams.algorithms.lsh.PeakListRandomProjection method) (dreams.utils.spectra.PeakListModifiedCosine method)

compute_pairwise() (dreams.utils.spectra.PeakListModifiedCosine method) compute_reset_metrics() (dreams.utils.annotation.FingerprintInChIRetrieval method) condense_dreams_knn() (in module dreams.utils.data) configure_optimizers() (dreams.models.baselines.deep_sets.DeepSetsPeaks method) (dreams.models.dreams.dreams.DreaMS method) (dreams.models.heads.heads.FineTuningHead method) CONSEQUENT_MSN (dreams.utils.lcms.MSLevelsOrder attribute) contains_similar() (in module dreams.utils.misc) ContrastiveHead (class in dreams.models.heads.heads) ContrastiveSpectraDataset (class in dreams.utils.data) ContrastiveValidation (class in dreams.utils.data) ConvolutionalBaseline (class in dreams.models.baselines.convolutional_baseline) CorrelationValidation (class in dreams.utils.data) CosSimLoss (class in dreams.models.optimization.losses_metrics) CSRKNN (class in dreams.utils.data) CVDataModule (class in dreams.utils.data)

D

data (dreams.utils.data.MaskedSpectraDataset attribute) DataFormat (class in dreams.utils.dformats) DataFormatA (class in dreams.utils.dformats) DataFormatA1 (class in dreams.utils.dformats) DataFormatA2 (class in dreams.utils.dformats) DataFormatA3 (class in dreams.utils.dformats) DataFormatB (class in dreams.utils.dformats) DataFormatBuilder (class in dreams.utils.dformats) DataFormatC (class in dreams.utils.dformats) decode_knn_i() (dreams.api.DreaMSAtlas method) DeepSets (class in dreams.models.baselines.deep_sets) DeepSetsPeakBinCls (class in dreams.models.baselines.deep_sets) DeepSetsPeakIntReg (class in dreams.models.baselines.deep_sets) DeepSetsPeakReg (class in dreams.models.baselines.deep_sets) DeepSetsPeaks (class in dreams.models.baselines.deep_sets) DeepSetsPeaksFingerprint (class in dreams.models.baselines.deep_sets) denormalize_prop() (dreams.utils.mols.MolPropertyCalculator method) denormalize_props() (dreams.utils.mols.MolPropertyCalculator method) deterministic_mask (dreams.utils.data.MaskedSpectraDataset attribute) df_to_MSnSpectra() (in module dreams.utils.spectra) dformat (dreams.utils.data.MaskedSpectraDataset attribute) (dreams.utils.data.SpectrumPreprocessor attribute) disable_rdkit_log() (in module dreams.utils.mols) distr_density() (in module dreams.utils.plots) download_pretrained_model() (in module dreams.utils.misc) downloadpublicdata_to_hdf5s() (in module dreams.utils.io) dreams module DreaMS (class in dreams.models.dreams.dreams) dreams.algorithms module dreams.algorithms.lsh module dreams.algorithms.lsh.lsh module dreams.algorithms.murcko_hist module dreams.algorithms.murcko_hist.murcko_hist module dreams.api module dreams.cli module dreams.definitions module dreams.models module dreams.models.baselines module dreams.models.baselines.convolutional_baseline module dreams.models.baselines.deep_sets module dreams.models.baselines.feed_forward_baseline module dreams.models.baselines.random_continuous_baseline module dreams.models.baselines.random_discrete_baseline module dreams.models.dreams module

dreams.models.dreams.dreams module dreams.models.dreams.layers module dreams.models.heads module dreams.models.heads.heads module dreams.models.layers module dreams.models.layers.feed_forward module dreams.models.layers.fourier_features module dreams.models.layers.fp_growing module dreams.models.layers.tnq_transformer module dreams.models.optimization module dreams.models.optimization.losses_metrics module dreams.models.optimization.samplers module dreams.models.optimization.schedulers module dreams.models.pretrained module dreams.training module dreams.training.train module dreams.training.train_argparse module dreams.utils module dreams.utils.annotation module dreams.utils.data module dreams.utils.dformats module dreams.utils.io module dreams.utils.lcms module dreams.utils.misc module dreams.utils.mols module dreams.utils.plots module dreams.utils.spectra module dreams_attn_scores() (in module dreams.api) dreams_embeddings() (in module dreams.api) dreams_intermediates() (in module dreams.api) dreams_predictions() (in module dreams.api) DreaMSAtlas (class in dreams.api) DreaMSSearch (class in dreams.api)

E

EMPTY (dreams.utils.lcms.MSLevelsOrder attribute) encode_knn_i() (dreams.api.DreaMSAtlas method) estimate_peak_list_type() (in module dreams.utils.lcms)

evaluate_split() (in module dreams.utils.data) export() (in module dreams.definitions) extend_column() (dreams.utils.data.MSData method)

F

FeedForward (class in dreams.models.dreams.layers) (class in dreams.models.layers.feed_forward) FeedForwardBaseline (class in dreams.models.baselines.feed_forward_baseline) FineTuningHead (class in dreams.models.heads.heads) FingerprintHead (class in dreams.models.heads.heads) FingerprintInChIRetrieval (class in dreams.utils.annotation) FingerprintMetrics (class in dreams.models.optimization.losses_metrics) flush() (dreams.utils.io.TqdmToLogger method) FocalLoss (class in dreams.models.optimization.losses_metrics) form_subset() (dreams.utils.data.MSData method) formula_is_carbohydrate() (in module dreams.utils.mols) formula_is_halogenated() (in module dreams.utils.mols) formula_to_dict() (in module dreams.utils.mols) formula_type() (in module dreams.utils.mols) forward() (dreams.models.baselines.convolutional_baseline.ConvolutionalBaseline method) (dreams.models.baselines.deep_sets.DeepSets method) (dreams.models.baselines.deep_sets.DeepSetsPeakBinCls method) (dreams.models.baselines.deep_sets.DeepSetsPeaks method) (dreams.models.baselines.feed_forward_baseline.FeedForwardBaseline method) (dreams.models.baselines.random_continuous_baseline.RandomContinuousBaseline method) (dreams.models.baselines.random_discrete_baseline.RandomDiscreteBaseline method) (dreams.models.dreams.dreams.DreaMS method) (dreams.models.dreams.layers.FeedForward method) (dreams.models.dreams.layers.MultiheadAttention method) (dreams.models.dreams.layers.ScaleNorm method) (dreams.models.dreams.layers.TransformerEncoder method) (dreams.models.heads.heads.FineTuningHead method) (dreams.models.layers.feed_forward.FeedForward method) (dreams.models.layers.fourier_features.FourierFeatures method) (dreams.models.layers.fp_growing.FPGrowingModule method) (dreams.models.optimization.losses_metrics.CosSimLoss method) (dreams.models.optimization.losses_metrics.FocalLoss method) (dreams.models.optimization.losses_metrics.SmoothIoULoss method)

FourierFeatures (class in dreams.models.layers.fourier_features) fp_func_from_str() (in module dreams.utils.mols) FPGrowingModule (class in dreams.models.layers.fp_growing) frac_masks (dreams.utils.data.MaskedSpectraDataset attribute) from_ckpt() (dreams.api.PreTrainedModel class method) from_edge_list() (dreams.utils.data.CSRKNN static method) from_hdf5() (dreams.utils.data.MSData static method) from_hdf5_chunks() (dreams.utils.data.MSData static method) from_hot() (in module dreams.utils.spectra) from_hot_logits() (in module dreams.utils.spectra) from_mgf() (dreams.utils.data.MSData static method) from_msp() (dreams.utils.data.MSData static method) from_mzml() (dreams.utils.data.MSData static method) from_mzxml() (dreams.utils.data.MSData static method) from_name() (dreams.api.PreTrainedModel class method) from_ngt_index() (dreams.utils.data.CSRKNN static method) from_npz() (dreams.utils.data.CSRKNN static method) from_pandas() (dreams.utils.data.MSData static method) from_pickle() (dreams.utils.data.MSData static method) ftp_to_msv_id() (in module dreams.utils.io)

G

gems_hf_download() (in module dreams.utils.misc) generate_fragments() (in module dreams.utils.mols) generate_spectrum() (in module dreams.utils.mols) get_adducts() (dreams.utils.data.MSData method) get_base_peak() (in module dreams.utils.spectra) get_charges() (dreams.utils.data.MSData method) get_closest_mz_peak() (in module dreams.utils.spectra) get_closest_mz_peaks() (in module dreams.utils.spectra) get_closest_values() (in module dreams.utils.misc) get_collision_energy() (dreams.utils.spectra.MSnSpectrum method) get_data() (dreams.api.DreaMSAtlas method) (dreams.utils.data.ImplExplValidation method) get_dformat() (dreams.utils.dformats.DataFormatBuilder method) get_embeddings() (dreams.models.dreams.dreams.DreaMS method) (in module dreams.models.dreams.dreams) get_highest_peaks() (in module dreams.utils.spectra) get_instrument_props() (in module dreams.utils.lcms) get_intensities() (dreams.utils.spectra.MSnSpectrum method) get_ionization_mode() (dreams.utils.spectra.MSnSpectrum method) get_labels() (dreams.utils.data.ContrastiveValidation method) get_lib_idx() (dreams.api.DreaMSAtlas method) get_lr() (dreams.models.optimization.schedulers.NoamScheduler method) get_lsh_cluster() (dreams.api.DreaMSAtlas method) get_mol_mass() (in module dreams.utils.mols) get_mzs() (dreams.utils.spectra.MSnSpectrum method) get_name() (dreams.utils.data.ContrastiveValidation method) get_nature_hex_colors() (in module dreams.utils.plots) get_neighbors() (dreams.api.DreaMSAtlas method) get_node_cluster() (dreams.api.DreaMSAtlas method)

get_node_repr() (dreams.api.DreaMSAtlas method) get_num_folds() (dreams.utils.data.CVDataModule method) get_num_peaks() (in module dreams.utils.spectra) get_order_of_spectra() (in module dreams.utils.lcms) get_palette() (in module dreams.utils.plots) get_peak_intens_nbhd() (in module dreams.utils.spectra) get_peak_list() (dreams.utils.spectra.MSnSpectrum method) get_peaks_n() (dreams.utils.spectra.MSnSpectrum method) get_prec_mzs() (dreams.utils.data.MSData method) get_precursor_charge() (dreams.utils.spectra.MSnSpectrum method) get_precursor_formula() (dreams.utils.spectra.MSnSpectrum method) get_precursor_mass() (dreams.utils.spectra.MSnSpectrum method) get_precursor_mol() (dreams.utils.spectra.MSnSpectrum method) get_precursor_mz() (dreams.utils.spectra.MSnSpectrum method) get_pwiz_stats() (in module dreams.utils.lcms) get_res() (dreams.utils.data.AttentionEntropyValidation method) (dreams.utils.data.ContrastiveValidation method) (dreams.utils.data.CorrelationValidation method) (dreams.utils.data.ImplExplValidation method) (dreams.utils.data.KNNValidation method) (dreams.utils.data.ManualValidation method) (dreams.utils.data.SpecRetrievalValidation method) get_smiles() (dreams.utils.data.MSData method) get_spec() (dreams.utils.data.MaskedSpectraDataset method), [1] get_spectra() (dreams.utils.data.MSData method) get_spectrum_type() (in module dreams.utils.lcms) get_tight_xics() (in module dreams.utils.lcms) get_umap_plot() (dreams.utils.data.ContrastiveValidation method) get_values() (dreams.utils.data.MSData method)

H

has_peak_at() (in module dreams.utils.spectra) head (dreams.models.heads.heads.BinClassificationHead attribute) (dreams.models.heads.heads.FineTuningHead attribute) (dreams.models.heads.heads.RegressionHead attribute) hf_download() (in module dreams.utils.misc)

high_intensity_thld (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatA2 attribute) (dreams.utils.dformats.DataFormatA3 attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute)

I

ImplExplValidation (class in dreams.utils.data) init_plotting() (in module dreams.utils.plots) intens_amplitude() (in module dreams.utils.spectra) interpolate_interval() (in module dreams.utils.misc) IntRegressionHead (class in dreams.models.heads.heads) inv_neighbors() (dreams.utils.data.CSRKNN method)

INVALID (dreams.utils.lcms.MSLevelsOrder attribute) (dreams.utils.lcms.SpecType attribute) is_float() (in module dreams.utils.misc) is_library_i() (dreams.api.DreaMSAtlas method) is_sorted() (in module dreams.utils.misc) is_valid_peak_list() (in module dreams.utils.spectra)

K

keys() (dreams.utils.io.ChunkedHDF5File method)

KNNValidation (class in dreams.utils.data)

L

LabeledSpectraDataset (class in dreams.utils.data) lcmsms_to_hdf5() (in module dreams.utils.io) level (dreams.utils.io.TqdmToLogger attribute) list_from_txt() (in module dreams.utils.io) list_to_txt() (in module dreams.utils.io) lists_to_legends() (in module dreams.utils.misc) load() (dreams.utils.data.MSData static method) load_col_in_mem() (dreams.utils.data.MSData method)

load_hdf5_in_mem() (dreams.utils.data.MSData method) (in module dreams.utils.data) logger (dreams.utils.io.TqdmToLogger attribute) loss (dreams.models.heads.heads.BinClassificationHead attribute) lr (dreams.models.heads.heads.FineTuningHead attribute) lsh_bin_size (dreams.utils.dformats.DataFormat attribute) lsh_n_hplanes (dreams.utils.dformats.DataFormat attribute) lsh_subset() (in module dreams.utils.io) lsh_weight (dreams.utils.data.MaskedSpectraDataset attribute)

M

maccs_fp() (in module dreams.utils.mols) main() (in module dreams.training.train) ManualValidation (class in dreams.utils.data) mask_intens_strategy (dreams.utils.data.MaskedSpectraDataset attribute) mask_peaks (dreams.utils.data.MaskedSpectraDataset attribute) mask_prec (dreams.utils.data.MaskedSpectraDataset attribute) mask_val (dreams.utils.data.MaskedSpectraDataset attribute) MaskedSpectraDataset (class in dreams.utils.data) MatchmsSpectraDataset (class in dreams.utils.data) max_charge (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) max_ms_level (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) max_mz (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) max_mz() (in module dreams.utils.spectra) max_peaks_n (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) max_prec_mz (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) max_tbxic_stdev (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) MaxVarBatchSampler (class in dreams.models.optimization.samplers) merge() (dreams.utils.data.MSData static method) merge_lcmsms_hdf5s() (in module dreams.utils.io) merge_ms_hdfs() (in module dreams.utils.io) merge_peak_lists() (in module dreams.utils.spectra) merge_stats() (in module dreams.utils.misc) metrics (dreams.models.heads.heads.BinClassificationHead attribute) min_charge (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatA3 attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) min_file_spectra (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) min_intensity_ampl (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatA2 attribute) (dreams.utils.dformats.DataFormatA3 attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute) min_mask_intens (dreams.utils.data.MaskedSpectraDataset attribute) min_n_masks (dreams.utils.data.MaskedSpectraDataset attribute) min_peaks_n (dreams.utils.dformats.DataFormat attribute) (dreams.utils.dformats.DataFormatA attribute) (dreams.utils.dformats.DataFormatA1 attribute) (dreams.utils.dformats.DataFormatA2 attribute) (dreams.utils.dformats.DataFormatA3 attribute) (dreams.utils.dformats.DataFormatB attribute) (dreams.utils.dformats.DataFormatC attribute)

MIXED_MSN (dreams.utils.lcms.MSLevelsOrder attribute) module dreams dreams.algorithms dreams.algorithms.lsh dreams.algorithms.lsh.lsh dreams.algorithms.murcko_hist dreams.algorithms.murcko_hist.murcko_hist dreams.api dreams.cli dreams.definitions dreams.models dreams.models.baselines dreams.models.baselines.convolutional_baseline dreams.models.baselines.deep_sets dreams.models.baselines.feed_forward_baseline dreams.models.baselines.random_continuous_baseline dreams.models.baselines.random_discrete_baseline dreams.models.dreams dreams.models.dreams.dreams dreams.models.dreams.layers dreams.models.heads dreams.models.heads.heads dreams.models.layers dreams.models.layers.feed_forward dreams.models.layers.fourier_features dreams.models.layers.fp_growing dreams.models.layers.tnq_transformer dreams.models.optimization dreams.models.optimization.losses_metrics dreams.models.optimization.samplers dreams.models.optimization.schedulers dreams.models.pretrained dreams.training dreams.training.train dreams.training.train_argparse dreams.utils dreams.utils.annotation dreams.utils.data dreams.utils.dformats dreams.utils.io dreams.utils.lcms dreams.utils.misc dreams.utils.mols dreams.utils.plots dreams.utils.spectra mol_props_calc (dreams.models.heads.heads.RegressionHead attribute) mol_to_formula() (in module dreams.utils.mols) mol_to_img_str() (in module dreams.utils.mols) mol_to_inchi14() (in module dreams.utils.mols) mol_to_props() (dreams.utils.mols.MolPropertyCalculator method) MolPropertyCalculator (class in dreams.utils.mols) morgan_fp() (in module dreams.utils.mols) morgan_mol_sim() (in module dreams.utils.mols) morgan_smiles_sim() (in module dreams.utils.mols) MSData (class in dreams.utils.data) MSLevelsOrder (class in dreams.utils.lcms) MSnSpectrum (class in dreams.utils.spectra) MultiheadAttention (class in dreams.models.dreams.layers) multirings() (in module dreams.algorithms.murcko_hist.murcko_hist) murcko_hist() (in module dreams.algorithms.murcko_hist) (in module dreams.algorithms.murcko_hist.murcko_hist) murcko_hists_dist() (in module dreams.algorithms.murcko_hist) (in module dreams.algorithms.murcko_hist.murcko_hist) mz_shift_aug_max (dreams.utils.data.SpectrumPreprocessor attribute) mz_shift_aug_p (dreams.utils.data.SpectrumPreprocessor attribute)

N

n_highest_peaks (dreams.utils.data.SpectrumPreprocessor attribute) n_samples (dreams.utils.data.MaskedSpectraDataset attribute) neighbors() (dreams.utils.data.CSRKNN method) networkx_to_dataframe() (in module dreams.utils.misc) NoamScheduler (class in dreams.models.optimization.schedulers) normalize_mzs (dreams.utils.data.SpectrumPreprocessor attribute) normalize_mzs() (in module dreams.utils.spectra)

normalize_prop() (dreams.utils.mols.MolPropertyCalculator method) normalize_props() (dreams.utils.mols.MolPropertyCalculator method) np_classify() (in module dreams.utils.mols) np_to_rdkit_fp() (in module dreams.utils.mols) num_features() (dreams.models.layers.fourier_features.FourierFeatures method) num_high_peaks() (in module dreams.utils.spectra) num_hot_classes() (in module dreams.utils.spectra)

O

on_train_batch_start() (dreams.utils.data.SSLProbingValidation method) on_train_epoch_start() (dreams.models.heads.heads.FineTuningHead method) on_validation_epoch_end() (dreams.models.dreams.dreams.DreaMS method) (dreams.models.heads.heads.BinClassificationHead method) (dreams.models.heads.heads.FingerprintHead method)

out_dim (dreams.models.heads.heads.RegressionHead attribute)

P

pad_peak_list() (in module dreams.utils.spectra) parse_args() (in module dreams.training.train_argparse) parse_raw_peak_list() (in module dreams.utils.spectra) parse_sirius_ms() (in module dreams.utils.io) parsed_lcmsms_to_hdf() (in module dreams.utils.io) PeakListModifiedCosine (class in dreams.utils.spectra) PeakListRandomProjection (class in dreams.algorithms.lsh) (class in dreams.algorithms.lsh.lsh) pie_chart() (in module dreams.utils.plots) plot_nx_graph() (in module dreams.utils.plots) plot_spectrum() (in module dreams.utils.spectra) prec_intens (dreams.utils.data.SpectrumPreprocessor attribute) precision (dreams.utils.data.SpectrumPreprocessor attribute) precursor_emb (dreams.models.heads.heads.FineTuningHead attribute)

predict_fluorine() (in module dreams.api) prepare_data_per_node (dreams.utils.data.CVDataModule attribute) (dreams.utils.data.RandomSplitDataModule attribute) (dreams.utils.data.SplittedDataModule attribute) prepend_precursor_peak() (in module dreams.utils.spectra) prepend_to_stem() (in module dreams.utils.io) PreTrainedModel (class in dreams.api) process_peak_list() (in module dreams.utils.spectra) PROFILE (dreams.utils.lcms.SpecType attribute) proj_k() (dreams.models.dreams.layers.MultiheadAttention method) proj_o() (dreams.models.dreams.layers.MultiheadAttention method) proj_q() (dreams.models.dreams.layers.MultiheadAttention method) proj_qkv() (dreams.models.dreams.layers.MultiheadAttention method) proj_v() (dreams.models.dreams.layers.MultiheadAttention method)

Q

query() (dreams.api.DreaMSSearch method)

R

RandomContinuousBaseline (class in dreams.models.baselines.random_continuous_baseline) RandomDiscreteBaseline (class in dreams.models.baselines.random_discrete_baseline) RandomProjection (class in dreams.algorithms.lsh.lsh) RandomSplitDataModule (class in dreams.utils.data) RawSpectraDataset (class in dreams.utils.data) rdkit_fp() (in module dreams.utils.mols) rdkit_fp_to_np() (in module dreams.utils.mols) rdkit_mol_sim() (in module dreams.utils.mols) rdkit_smiles_sim() (in module dreams.utils.mols) read_json() (in module dreams.utils.io) read_json_spec() (in module dreams.utils.io) read_lcmsms() (in module dreams.utils.io) read_mgf() (in module dreams.utils.io) read_ms() (in module dreams.utils.io)

read_msp() (in module dreams.utils.io) read_mzml() (in module dreams.utils.io) read_pickle() (in module dreams.utils.io) read_textual_ms_format() (in module dreams.utils.io) RegressionHead (class in dreams.models.heads.heads) remove_column() (dreams.utils.data.MSData method) remove_electromagnetic_spectra() (in module dreams.utils.lcms) remove_unused_backbone_parameters() (dreams.api.PreTrainedModel method) rename_column() (dreams.utils.data.MSData method) ret_order_pairs (dreams.utils.data.MaskedSpectraDataset attribute) retrieve() (dreams.utils.annotation.SpectralLibraryRetrieval method) retrieve_df() (dreams.utils.annotation.SpectralLibraryRetrieval method) retrieve_inchi14s() (dreams.utils.annotation.FingerprintInChIRetrieval method) return_charge (dreams.utils.data.MaskedSpectraDataset attribute) rgb_to_hex() (in module dreams.utils.plots)

S

sample_hdf() (in module dreams.utils.io) save_fig() (in module dreams.utils.plots) save_nist_like_df_to_mgf() (in module dreams.utils.io) savefig() (in module dreams.utils.io) ScaleNorm (class in dreams.models.dreams.layers) serialize() (in module dreams.cli) set_model_gains() (dreams.utils.data.ImplExplValidation method) setup_fold_index() (dreams.utils.data.CVDataModule method) setup_logger() (in module dreams.utils.io) shape (dreams.utils.io.ChunkedDatasetAccessor property) show_mols() (in module dreams.utils.mols) sigmoid (dreams.models.heads.heads.RegressionHead attribute) SINGLE_MS1 (dreams.utils.lcms.MSLevelsOrder attribute) SINGLE_MSN (dreams.utils.lcms.MSLevelsOrder attribute) SIZE_OF_SPECTRUMTYPE (dreams.utils.lcms.SpecType attribute) smiles_to_formula() (in module dreams.utils.mols) smiles_to_inchi14() (in module dreams.utils.mols) SmoothIoULoss (class in dreams.models.optimization.losses_metrics) sort_by_rt() (in module dreams.utils.lcms) sorted_by_rt() (in module dreams.utils.lcms) spec_entropy_cleaning (dreams.utils.data.SpectrumPreprocessor attribute) spec_preproc (dreams.utils.data.MaskedSpectraDataset attribute)

spec_ssl_step() (dreams.models.dreams.dreams.DreaMS method) spec_to_matchms() (dreams.utils.data.MSData method) SpecRetrievalValidation (class in dreams.utils.data) SpectralLibraryRetrieval (class in dreams.utils.annotation) SpectrumPreprocessor (class in dreams.utils.data) SpecType (class in dreams.utils.lcms) SplittedDataModule (class in dreams.utils.data) ssl_objective (dreams.utils.data.MaskedSpectraDataset attribute) SSLProbingValidation (class in dreams.utils.data) standartize_gnps_species() (in module dreams.utils.lcms) step() (dreams.models.baselines.deep_sets.DeepSetsPeakBinCls method) (dreams.models.baselines.deep_sets.DeepSetsPeakReg method) (dreams.models.baselines.deep_sets.DeepSetsPeaks method) (dreams.models.baselines.deep_sets.DeepSetsPeaksFingerprint method) (dreams.models.dreams.dreams.DreaMS method) (dreams.models.heads.heads.BinClassificationHead method) (dreams.models.heads.heads.ContrastiveHead method) (dreams.models.heads.heads.FineTuningHead method) (dreams.models.heads.heads.FingerprintHead method) (dreams.models.heads.heads.RegressionHead method) subset_lsh() (in module dreams.utils.data) suppress_output() (in module dreams.utils.io)

T

tanimoto_sim() (in module dreams.utils.mols) test_dataloader() (dreams.utils.data.RandomSplitDataModule method) (dreams.utils.data.SplittedDataModule method) THRESHOLDED (dreams.utils.lcms.SpecType attribute) to_A_format() (in module dreams.utils.dformats) to_classes() (in module dreams.utils.spectra) to_edge_list() (dreams.utils.data.CSRKNN method) to_format() (in module dreams.utils.dformats) to_graph() (dreams.utils.data.CSRKNN method) to_hot() (in module dreams.utils.spectra) to_matchms() (dreams.utils.data.MSData method) to_mgf() (dreams.utils.data.MSData method) to_npz() (dreams.utils.data.CSRKNN method) to_pandas() (dreams.utils.data.MSData method)

to_pynndescent() (dreams.utils.data.MSData method) to_rel_intensity() (in module dreams.utils.spectra) to_relative_intensities (dreams.utils.data.SpectrumPreprocessor attribute) to_torch_dataset() (dreams.utils.data.MSData method) TqdmToLogger (class in dreams.utils.io) train_dataloader() (dreams.utils.data.CVDataModule method) (dreams.utils.data.RandomSplitDataModule method) (dreams.utils.data.SplittedDataModule method) training_step() (dreams.models.baselines.deep_sets.DeepSetsPeaks method) (dreams.models.dreams.dreams.DreaMS method) (dreams.models.heads.heads.BinClassificationHead method) (dreams.models.heads.heads.ContrastiveHead method) (dreams.models.heads.heads.FineTuningHead method) TransformerEncoder (class in dreams.models.dreams.layers) trim_peak_list() (in module dreams.utils.spectra)

U

unfreeze_backbone_at_epoch (dreams.models.heads.heads.FineTuningHead attribute) UNIFORM_MS1 (dreams.utils.lcms.MSLevelsOrder attribute) UNIFORM_MSN (dreams.utils.lcms.MSLevelsOrder attribute)

UNKNOWN (dreams.utils.lcms.SpecType attribute) unpad_peak_list() (in module dreams.utils.spectra) use_col_as_index() (dreams.utils.data.MSData method)

V

val_dataloader() (dreams.utils.data.CVDataModule method) (dreams.utils.data.RandomSplitDataModule method) (dreams.utils.data.SplittedDataModule method) val_prep_args() (in module dreams.training.train_argparse) val_spec() (dreams.utils.dformats.DataFormat method) validate() (dreams.models.heads.heads.FingerprintHead method) validation_step() (dreams.models.baselines.deep_sets.DeepSetsPeakBinCls method) (dreams.models.baselines.deep_sets.DeepSetsPeakIntReg method) (dreams.models.baselines.deep_sets.DeepSetsPeakReg method) (dreams.models.baselines.deep_sets.DeepSetsPeaks method) (dreams.models.baselines.deep_sets.DeepSetsPeaksFingerprint method) (dreams.models.dreams.dreams.DreaMS method) (dreams.models.heads.heads.BinClassificationHead method) (dreams.models.heads.heads.ContrastiveHead method) (dreams.models.heads.heads.FineTuningHead method) (dreams.models.heads.heads.FingerprintHead method) (dreams.models.heads.heads.IntRegressionHead method) (dreams.models.heads.heads.RegressionHead method)

W

wandb_import() (in module dreams.utils.io) weight_decay (dreams.models.heads.heads.FineTuningHead attribute)

write() (dreams.utils.io.TqdmToLogger method) write_json() (in module dreams.utils.io) write_pickle() (in module dreams.utils.io)