Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | W | X | Z _ __init__() (peptdeep.mass_spec.mass_calibration.MassCalibratorForRT_KNN method) (peptdeep.mass_spec.match.PepSpecMatch method) (peptdeep.mass_spec.ms_reader.MSReaderBase method) (peptdeep.mass_spec.ms_reader.MSReaderProvider method) (peptdeep.mass_spec.ms_reader.ThermoRawMS1Reader method) (peptdeep.mass_spec.ms_reader.ThermoRawMS2Reader method) (peptdeep.model.building_block.AA_Mod_Embedding method) (peptdeep.model.building_block.Decoder_GRU method) (peptdeep.model.building_block.Decoder_Linear method) (peptdeep.model.building_block.Decoder_LSTM method) (peptdeep.model.building_block.Encoder_26AA_Mod_Charge_CNN_LSTM_AttnSum method) (peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM method) (peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM_AttnSum method) (peptdeep.model.building_block.Encoder_26AA_Mod_LSTM method) (peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer method) (peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer_AttnSum method) (peptdeep.model.building_block.Encoder_AA_Mod_CNN_LSTM_AttnSum method) (peptdeep.model.building_block.Encoder_AA_Mod_Transformer method) (peptdeep.model.building_block.Encoder_AA_Mod_Transformer_AttnSum method) (peptdeep.model.building_block.HFace_Transformer_with_PositionalEncoder method) (peptdeep.model.building_block.Hidden_HFace_Transformer method) (peptdeep.model.building_block.Hidden_Transformer method) (peptdeep.model.building_block.Input_26AA_Mod_Charge_LSTM method) (peptdeep.model.building_block.Input_26AA_Mod_LSTM method) (peptdeep.model.building_block.Input_26AA_Mod_Meta_LSTM method) (peptdeep.model.building_block.Input_26AA_Mod_PositionalEncoding method) (peptdeep.model.building_block.Input_AA_Mod_Charge_PositionalEncoding method) (peptdeep.model.building_block.Input_AA_Mod_PositionalEncoding method) (peptdeep.model.building_block.Meta_Embedding method) (peptdeep.model.building_block.Mod_Embedding method) (peptdeep.model.building_block.Mod_Embedding_FixFirstK method) (peptdeep.model.building_block.PositionalEmbedding method) (peptdeep.model.building_block.PositionalEncoding method) (peptdeep.model.building_block.Seq_Meta_Linear method) (peptdeep.model.building_block.Seq_Meta_LSTM method) (peptdeep.model.building_block.Seq_Transformer method) (peptdeep.model.building_block.SeqAttentionSum method) (peptdeep.model.building_block.SeqCNN method) (peptdeep.model.building_block.SeqCNN_MultiKernel method) (peptdeep.model.building_block.SeqGRU method) (peptdeep.model.building_block.SeqLSTM method) (peptdeep.model.ccs.AlphaCCSModel method) (peptdeep.model.ccs.Model_CCS_Bert method) (peptdeep.model.ccs.Model_CCS_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_BinaryClassification_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_BinaryClassification_Transformer method) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_Regression_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_Regression_Transformer method) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_BinaryClassification_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_BinaryClassification_Transformer method) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_Regression_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_Regression_Transformer method) (peptdeep.model.generic_property_prediction.ModelInterface_for_Generic_AASeq_BinaryClassification method) (peptdeep.model.generic_property_prediction.ModelInterface_for_Generic_AASeq_MultiLabelClassification method) (peptdeep.model.generic_property_prediction.ModelInterface_for_Generic_AASeq_Regression method) (peptdeep.model.generic_property_prediction.ModelInterface_for_Generic_ModAASeq_BinaryClassification method) (peptdeep.model.generic_property_prediction.ModelInterface_for_Generic_ModAASeq_MultiLabelClassification method) (peptdeep.model.generic_property_prediction.ModelInterface_for_Generic_ModAASeq_Regression method) (peptdeep.model.model_interface.LR_SchedulerInterface method) (peptdeep.model.model_interface.ModelInterface method) (peptdeep.model.model_interface.WarmupLR_Scheduler method) (peptdeep.model.ms2.IntenAwareLoss method) (peptdeep.model.ms2.ModelMS2Bert method) (peptdeep.model.ms2.ModelMS2pDeep method) (peptdeep.model.ms2.ModelMS2Transformer method) (peptdeep.model.ms2.pDeepModel method) (peptdeep.model.rt.AlphaRTModel method) (peptdeep.model.rt.Model_RT_Bert method) (peptdeep.model.rt.Model_RT_LSTM_CNN method) (peptdeep.pretrained_models.ModelManager method) (peptdeep.protein.fasta.PredictSpecLibFasta method) (peptdeep.rescore.feature_extractor.ScoreFeatureExtractor method) (peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP method) (peptdeep.spec_lib.library_factory.LibraryMakerProvider method) (peptdeep.spec_lib.library_factory.PredictLibraryMakerBase method) (peptdeep.spec_lib.predict_lib.PredictSpecLib method) (peptdeep.spec_lib.predict_lib.PredictSpecLibFlat method) A aa_embedding() (in module peptdeep.model.building_block) AA_Mod_Embedding (class in peptdeep.model.building_block) aa_one_hot() (in module peptdeep.model.building_block) AATransformerEncoding (in module peptdeep.model.building_block) add_charge() (peptdeep.protein.fasta.PredictSpecLibFasta method) add_cutoff_metric() (in module peptdeep.model.ms2) add_irt_column_to_precursor_df() (peptdeep.model.rt.AlphaRTModel method) add_user_defined_modifications() (in module peptdeep.settings) AlphaCCSModel (class in peptdeep.model.ccs) AlphaPept_HDF_MS1_Reader (class in peptdeep.mass_spec.ms_reader) AlphaPept_HDF_MS2_Reader (class in peptdeep.mass_spec.ms_reader) AlphaRTModel (class in peptdeep.model.rt) append_nAA_column_if_missing() (in module peptdeep.model.model_interface) ascii_embedding() (in module peptdeep.model.building_block) B batch_callback() (peptdeep.model.model_interface.CallbackHandler method) bootstrap_nce_search() (peptdeep.model.ms2.pDeepModel method) build() (peptdeep.model.model_interface.ModelInterface method) build_from_py_codes() (peptdeep.model.model_interface.ModelInterface method) build_spectrum_df() (peptdeep.mass_spec.ms_reader.MSReaderBase method) C calc_fdr() (in module peptdeep.rescore.fdr) calc_fdr_for_df() (in module peptdeep.rescore.fdr) calc_fdr_from_ref() (in module peptdeep.rescore.fdr) calc_fdr_from_ref_for_df() (in module peptdeep.rescore.fdr) calc_ms2_similarity() (in module peptdeep.model.ms2) calibrate() (peptdeep.mass_spec.mass_calibration.MassCalibratorForRT_KNN method) calibrate_one() (in module peptdeep.mass_spec.mass_calibration) CallbackHandler (class in peptdeep.model.model_interface) ccs_model (peptdeep.pretrained_models.ModelManager attribute) ccs_to_mobility_pred() (peptdeep.model.ccs.AlphaCCSModel method) ccs_to_mobility_pred_df() (in module peptdeep.model.ccs) charged_frags_to_tensor() (in module peptdeep.model.ms2) clear_error_modloss_intensities() (in module peptdeep.pretrained_models) count_mods() (in module peptdeep.pretrained_models) D Decoder_GRU (class in peptdeep.model.building_block) Decoder_Linear (class in peptdeep.model.building_block) Decoder_LSTM (class in peptdeep.model.building_block) device (peptdeep.model.model_interface.ModelInterface property) device_ids (peptdeep.model.model_interface.ModelInterface property) device_type (peptdeep.model.model_interface.ModelInterface property) download_models() (in module peptdeep.pretrained_models) E Encoder_26AA_Mod_Charge_CNN_LSTM_AttnSum (class in peptdeep.model.building_block) Encoder_26AA_Mod_CNN_LSTM (class in peptdeep.model.building_block) Encoder_26AA_Mod_CNN_LSTM_AttnSum (class in peptdeep.model.building_block) Encoder_26AA_Mod_LSTM (class in peptdeep.model.building_block) Encoder_AA_Mod_Charge_Transformer (class in peptdeep.model.building_block) Encoder_AA_Mod_Charge_Transformer_AttnSum (class in peptdeep.model.building_block) Encoder_AA_Mod_CNN_LSTM_AttnSum (class in peptdeep.model.building_block) Encoder_AA_Mod_Transformer (class in peptdeep.model.building_block) Encoder_AA_Mod_Transformer_AttnSum (class in peptdeep.model.building_block) epoch_callback() (peptdeep.model.model_interface.CallbackHandler method) epoch_to_train_ms2 (peptdeep.pretrained_models.ModelManager attribute) epoch_to_train_rt_ccs (peptdeep.pretrained_models.ModelManager attribute) extract_features() (peptdeep.rescore.feature_extractor.ScoreFeatureExtractor method) (peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP method) extract_features_one_raw() (peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP method) extract_features_one_raw_mp() (peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP method) extract_mobility_features() (peptdeep.rescore.feature_extractor.ScoreFeatureExtractor method) extract_rt_features() (peptdeep.rescore.feature_extractor.ScoreFeatureExtractor method) F FastaLibraryMaker (class in peptdeep.spec_lib.library_factory) fdr_from_ref() (in module peptdeep.rescore.fdr) fdr_to_q_values() (in module peptdeep.rescore.fdr) find_line() (in module peptdeep.mass_spec.ms_reader) fine_tune_models() (peptdeep.rescore.feature_extractor.ScoreFeatureExtractor method) (peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP method) fit() (peptdeep.mass_spec.mass_calibration.MassCalibratorForRT_KNN method) fixed_sequence_len (peptdeep.model.model_interface.ModelInterface property) forward() (peptdeep.model.building_block.AA_Mod_Embedding method) (peptdeep.model.building_block.Decoder_GRU method) (peptdeep.model.building_block.Decoder_Linear method) (peptdeep.model.building_block.Decoder_LSTM method) (peptdeep.model.building_block.Encoder_26AA_Mod_Charge_CNN_LSTM_AttnSum method) (peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM method) (peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM_AttnSum method) (peptdeep.model.building_block.Encoder_26AA_Mod_LSTM method) (peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer method) (peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer_AttnSum method) (peptdeep.model.building_block.Encoder_AA_Mod_CNN_LSTM_AttnSum method) (peptdeep.model.building_block.Encoder_AA_Mod_Transformer method) (peptdeep.model.building_block.Encoder_AA_Mod_Transformer_AttnSum method) (peptdeep.model.building_block.HFace_Transformer_with_PositionalEncoder method) (peptdeep.model.building_block.Hidden_HFace_Transformer method) (peptdeep.model.building_block.Hidden_Transformer method) (peptdeep.model.building_block.Input_26AA_Mod_Charge_LSTM method) (peptdeep.model.building_block.Input_26AA_Mod_LSTM method) (peptdeep.model.building_block.Input_26AA_Mod_Meta_LSTM method) (peptdeep.model.building_block.Input_26AA_Mod_PositionalEncoding method) (peptdeep.model.building_block.Input_AA_Mod_Charge_PositionalEncoding method) (peptdeep.model.building_block.Input_AA_Mod_PositionalEncoding method) (peptdeep.model.building_block.Meta_Embedding method) (peptdeep.model.building_block.Mod_Embedding method) (peptdeep.model.building_block.Mod_Embedding_FixFirstK method) (peptdeep.model.building_block.PositionalEmbedding method) (peptdeep.model.building_block.PositionalEncoding method) (peptdeep.model.building_block.Seq_Meta_Linear method) (peptdeep.model.building_block.Seq_Meta_LSTM method) (peptdeep.model.building_block.Seq_Transformer method) (peptdeep.model.building_block.SeqAttentionSum method) (peptdeep.model.building_block.SeqCNN method) (peptdeep.model.building_block.SeqCNN_MultiKernel method) (peptdeep.model.building_block.SeqGRU method) (peptdeep.model.building_block.SeqLSTM method) (peptdeep.model.ccs.Model_CCS_Bert method) (peptdeep.model.ccs.Model_CCS_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_BinaryClassification_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_BinaryClassification_Transformer method) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_Regression_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_Regression_Transformer method) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_BinaryClassification_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_BinaryClassification_Transformer method) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_Regression_LSTM method) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_Regression_Transformer method) (peptdeep.model.ms2.IntenAwareLoss method) (peptdeep.model.ms2.ModelMS2Bert method) (peptdeep.model.ms2.ModelMS2pDeep method) (peptdeep.model.ms2.ModelMS2Transformer method) (peptdeep.model.rt.Model_RT_Bert method) (peptdeep.model.rt.Model_RT_LSTM_CNN method) fragment_intensity_df (peptdeep.spec_lib.library_factory.PredictLibraryMakerBase property) fragment_mz_df (peptdeep.spec_lib.library_factory.PredictLibraryMakerBase property) G generate_library() (in module peptdeep.pipeline_api) get_ascii_indices() (in module peptdeep.model.featurize) get_batch_aa_indices() (in module peptdeep.model.featurize) get_batch_mod_feature() (in module peptdeep.model.featurize) get_cosine_schedule_with_warmup() (peptdeep.model.model_interface.WarmupLR_Scheduler method) get_fragment_median() (in module peptdeep.mass_spec.mass_calibration) get_fragment_mz_df() (peptdeep.mass_spec.match.PepSpecMatch method) get_last_lr() (peptdeep.model.model_interface.LR_SchedulerInterface method) (peptdeep.model.model_interface.WarmupLR_Scheduler method) get_local_model_zip_name() (in module peptdeep.pretrained_models) get_maker() (peptdeep.spec_lib.library_factory.LibraryMakerProvider method) get_median_pccs_for_dia_psms() (in module peptdeep.pipeline_api) get_model_download_instructions() (in module peptdeep.pretrained_models) get_model_url() (in module peptdeep.pretrained_models) get_model_zip_file_path() (in module peptdeep.pretrained_models) get_ms2_features() (in module peptdeep.rescore.feature_extractor) get_ms2_features_mp() (in module peptdeep.rescore.feature_extractor) get_parameter_num() (peptdeep.model.model_interface.ModelInterface method) get_peaks() (peptdeep.mass_spec.ms_reader.MSReaderBase method) get_peaks_by_scan_num() (peptdeep.mass_spec.ms_reader.MSReaderBase method) get_pretrain_dir() (in module peptdeep.pretrained_models) get_psm_scores() (in module peptdeep.rescore.feature_extractor) get_reader() (peptdeep.mass_spec.ms_reader.MSReaderProvider method) global_settings (in module peptdeep.settings) grid_nce_search() (peptdeep.model.ms2.pDeepModel method) H HFace_Transformer_with_PositionalEncoder (class in peptdeep.model.building_block) Hidden_HFace_Transformer (class in peptdeep.model.building_block) Hidden_Transformer (class in peptdeep.model.building_block) HiddenBert (in module peptdeep.model.building_block) I import_psm_df() (in module peptdeep.pipeline_api) index_ragged_list() (in module peptdeep.mass_spec.ms_reader) init_state() (in module peptdeep.model.building_block) Input_26AA_Mod_Charge_LSTM (class in peptdeep.model.building_block) Input_26AA_Mod_LSTM (class in peptdeep.model.building_block) Input_26AA_Mod_Meta_LSTM (class in peptdeep.model.building_block) Input_26AA_Mod_PositionalEncoding (class in peptdeep.model.building_block) Input_AA_CNN_Encoder (in module peptdeep.model.building_block) Input_AA_CNN_LSTM_cat_Charge_Encoder (in module peptdeep.model.building_block) Input_AA_CNN_LSTM_Encoder (in module peptdeep.model.building_block) Input_AA_LSTM_Encoder (in module peptdeep.model.building_block) Input_AA_Mod_Charge_PositionalEncoding (class in peptdeep.model.building_block) Input_AA_Mod_PositionalEncoding (class in peptdeep.model.building_block) InputAAEmbedding (in module peptdeep.model.building_block) InputAALSTM (in module peptdeep.model.building_block) InputAALSTM_cat_Charge (in module peptdeep.model.building_block) InputAALSTM_cat_Meta (in module peptdeep.model.building_block) InputMetaNet (in module peptdeep.model.building_block) InputModNet (in module peptdeep.model.building_block) InputModNetFixFirstK (in module peptdeep.model.building_block) instrument (peptdeep.pretrained_models.ModelManager attribute) (peptdeep.pretrained_models.ModelManager property) instrument_embedding() (in module peptdeep.model.building_block) IntenAwareLoss (class in peptdeep.model.ms2) invert_attention_mask() (in module peptdeep.model.building_block) is_model_zip() (in module peptdeep.pretrained_models) is_pfind_mgf() (in module peptdeep.mass_spec.ms_reader) L LibraryMakerProvider (class in peptdeep.spec_lib.library_factory) LinearDecoder (in module peptdeep.model.building_block) load() (peptdeep.mass_spec.ms_reader.AlphaPept_HDF_MS1_Reader method) (peptdeep.mass_spec.ms_reader.AlphaPept_HDF_MS2_Reader method) (peptdeep.mass_spec.ms_reader.MGFReader method) (peptdeep.mass_spec.ms_reader.MSReaderBase method) (peptdeep.mass_spec.ms_reader.MZMLReader method) (peptdeep.mass_spec.ms_reader.ThermoRawMS1Reader method) (peptdeep.mass_spec.ms_reader.ThermoRawMS2Reader method) (peptdeep.model.model_interface.ModelInterface method) load_dfs() (in module peptdeep.spec_lib.library_factory) load_external_models() (peptdeep.pretrained_models.ModelManager method) load_global_settings() (in module peptdeep.settings) load_installed_models() (peptdeep.pretrained_models.ModelManager method) load_models() (in module peptdeep.pretrained_models) load_models_by_model_type_in_zip() (in module peptdeep.pretrained_models) load_phos_models() (in module peptdeep.pretrained_models) LR_SchedulerInterface (class in peptdeep.model.model_interface) M make_library() (peptdeep.spec_lib.library_factory.PredictLibraryMakerBase method) MassCalibratorForRT_KNN (class in peptdeep.mass_spec.mass_calibration) match_centroid_mz() (in module peptdeep.mass_spec.match) match_first_last_profile_mz() (in module peptdeep.mass_spec.match) match_ms2() (peptdeep.rescore.feature_extractor.ScoreFeatureExtractor method) match_ms2_centroid() (peptdeep.mass_spec.match.PepSpecMatch method) match_ms2_one_raw() (peptdeep.mass_spec.match.PepSpecMatch method) match_one_raw() (in module peptdeep.rescore.feature_extractor) match_one_raw_mp() (in module peptdeep.rescore.feature_extractor) match_one_raw_with_numba() (in module peptdeep.mass_spec.match) match_profile_mz() (in module peptdeep.mass_spec.match) match_psms() (in module peptdeep.pipeline_api) Meta_Embedding (class in peptdeep.model.building_block) MGFReader (class in peptdeep.mass_spec.ms_reader) min_pred_value (peptdeep.model.model_interface.ModelInterface property) mobility_to_ccs_df_() (in module peptdeep.model.ccs) Mod_Embedding (class in peptdeep.model.building_block) Mod_Embedding_FixFirstK (class in peptdeep.model.building_block) Model_CCS_Bert (class in peptdeep.model.ccs) Model_CCS_LSTM (class in peptdeep.model.ccs) Model_for_Generic_AASeq_BinaryClassification_LSTM (class in peptdeep.model.generic_property_prediction) Model_for_Generic_AASeq_BinaryClassification_Transformer (class in peptdeep.model.generic_property_prediction) Model_for_Generic_AASeq_Regression_LSTM (class in peptdeep.model.generic_property_prediction) Model_for_Generic_AASeq_Regression_Transformer (class in peptdeep.model.generic_property_prediction) Model_for_Generic_ModAASeq_BinaryClassification_LSTM (class in peptdeep.model.generic_property_prediction) Model_for_Generic_ModAASeq_BinaryClassification_Transformer (class in peptdeep.model.generic_property_prediction) Model_for_Generic_ModAASeq_Regression_LSTM (class in peptdeep.model.generic_property_prediction) Model_for_Generic_ModAASeq_Regression_Transformer (class in peptdeep.model.generic_property_prediction) Model_RT_Bert (class in peptdeep.model.rt) Model_RT_LSTM (in module peptdeep.model.rt) Model_RT_LSTM_CNN (class in peptdeep.model.rt) ModelInterface (class in peptdeep.model.model_interface) ModelInterface_for_Generic_AASeq_BinaryClassification (class in peptdeep.model.generic_property_prediction) ModelInterface_for_Generic_AASeq_MultiLabelClassification (class in peptdeep.model.generic_property_prediction) ModelInterface_for_Generic_AASeq_MultiTargetClassification (in module peptdeep.model.generic_property_prediction) ModelInterface_for_Generic_AASeq_Regression (class in peptdeep.model.generic_property_prediction) ModelInterface_for_Generic_ModAASeq_BinaryClassification (class in peptdeep.model.generic_property_prediction) ModelInterface_for_Generic_ModAASeq_MultiLabelClassification (class in peptdeep.model.generic_property_prediction) ModelInterface_for_Generic_ModAASeq_MultiTargetClassification (in module peptdeep.model.generic_property_prediction) ModelInterface_for_Generic_ModAASeq_Regression (class in peptdeep.model.generic_property_prediction) ModelManager (class in peptdeep.pretrained_models) ModelMS2Bert (class in peptdeep.model.ms2) ModelMS2pDeep (class in peptdeep.model.ms2) ModelMS2Transformer (class in peptdeep.model.ms2) module peptdeep.mass_spec.mass_calibration peptdeep.mass_spec.match peptdeep.mass_spec.ms_reader peptdeep.model.building_block peptdeep.model.ccs peptdeep.model.featurize peptdeep.model.generic_property_prediction peptdeep.model.model_interface peptdeep.model.ms2 peptdeep.model.rt peptdeep.pipeline_api peptdeep.pretrained_models peptdeep.protein.fasta peptdeep.rescore.fdr peptdeep.rescore.feature_extractor peptdeep.settings peptdeep.spec_lib.library_factory peptdeep.spec_lib.predict_lib peptdeep.spec_lib.translate ms2_model (peptdeep.pretrained_models.ModelManager attribute) MSReaderBase (class in peptdeep.mass_spec.ms_reader) MSReaderProvider (class in peptdeep.mass_spec.ms_reader) MZMLReader (class in peptdeep.mass_spec.ms_reader) N nce (peptdeep.pretrained_models.ModelManager attribute) normalize_fragment_intensities() (in module peptdeep.model.ms2) O output_attentions (peptdeep.model.ccs.Model_CCS_Bert property) (peptdeep.model.generic_property_prediction.Model_for_Generic_AASeq_Regression_Transformer property) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_BinaryClassification_Transformer property) (peptdeep.model.generic_property_prediction.Model_for_Generic_ModAASeq_Regression_Transformer property) (peptdeep.model.ms2.ModelMS2Bert property) (peptdeep.model.rt.Model_RT_Bert property) OutputLinear_cat_Meta (in module peptdeep.model.building_block) OutputLSTM_cat_Meta (in module peptdeep.model.building_block) P parse_instrument_indices() (in module peptdeep.model.featurize) parse_mod_feature() (in module peptdeep.model.featurize) parse_pfind_scan_from_TITLE() (in module peptdeep.mass_spec.ms_reader) pDeepModel (class in peptdeep.model.ms2) pearson() (in module peptdeep.model.ms2) pearson_correlation() (in module peptdeep.model.ms2) PepSpecMatch (class in peptdeep.mass_spec.match) peptdeep.mass_spec.mass_calibration module peptdeep.mass_spec.match module peptdeep.mass_spec.ms_reader module peptdeep.model.building_block module peptdeep.model.ccs module peptdeep.model.featurize module peptdeep.model.generic_property_prediction module peptdeep.model.model_interface module peptdeep.model.ms2 module peptdeep.model.rt module peptdeep.pipeline_api module peptdeep.pretrained_models module peptdeep.protein.fasta module peptdeep.rescore.fdr module peptdeep.rescore.feature_extractor module peptdeep.settings module peptdeep.spec_lib.library_factory module peptdeep.spec_lib.predict_lib module peptdeep.spec_lib.translate module PeptideLibraryMaker (class in peptdeep.spec_lib.library_factory) PositionalEmbedding (class in peptdeep.model.building_block) PositionalEncoding (class in peptdeep.model.building_block) precursor_df (peptdeep.spec_lib.library_factory.PredictLibraryMakerBase property) PrecursorLibraryMaker (class in peptdeep.spec_lib.library_factory) predict() (peptdeep.model.model_interface.ModelInterface method) (peptdeep.model.ms2.pDeepModel method) predict_all() (peptdeep.pretrained_models.ModelManager method) (peptdeep.spec_lib.predict_lib.PredictSpecLib method) predict_all_mp() (peptdeep.pretrained_models.ModelManager method) predict_and_parse_lib_in_batch() (peptdeep.spec_lib.predict_lib.PredictSpecLibFlat method) predict_charge() (peptdeep.pretrained_models.ModelManager method) predict_mobility() (peptdeep.pretrained_models.ModelManager method) predict_mp() (peptdeep.model.model_interface.ModelInterface method) (peptdeep.model.ms2.pDeepModel method) predict_ms2() (peptdeep.pretrained_models.ModelManager method) predict_rt() (peptdeep.pretrained_models.ModelManager method) PredictLibraryMakerBase (class in peptdeep.spec_lib.library_factory) PredictSpecLib (class in peptdeep.spec_lib.predict_lib) PredictSpecLibFasta (class in peptdeep.protein.fasta) PredictSpecLibFlat (class in peptdeep.spec_lib.predict_lib) psm_num_to_train_ms2 (peptdeep.pretrained_models.ModelManager attribute) psm_num_to_train_rt_ccs (peptdeep.pretrained_models.ModelManager attribute) psm_sampling_with_important_mods() (in module peptdeep.pretrained_models) PSMReaderLibraryMaker (class in peptdeep.spec_lib.library_factory) R read_until() (in module peptdeep.mass_spec.ms_reader) register_maker() (peptdeep.spec_lib.library_factory.LibraryMakerProvider method) register_reader() (peptdeep.mass_spec.ms_reader.MSReaderProvider method) reinitialize_ms2_model() (peptdeep.pretrained_models.ModelManager method) reset_by_global_settings() (peptdeep.pretrained_models.ModelManager method) (peptdeep.rescore.feature_extractor.ScoreFeatureExtractor method) rt_model (peptdeep.pretrained_models.ModelManager attribute) S save() (peptdeep.model.model_interface.ModelInterface method) save_models() (peptdeep.pretrained_models.ModelManager method) ScoreFeatureExtractor (class in peptdeep.rescore.feature_extractor) ScoreFeatureExtractorMP (class in peptdeep.rescore.feature_extractor) Seq_Meta_Linear (class in peptdeep.model.building_block) Seq_Meta_LSTM (class in peptdeep.model.building_block) Seq_Transformer (class in peptdeep.model.building_block) SeqAttentionSum (class in peptdeep.model.building_block) SeqCNN (class in peptdeep.model.building_block) SeqCNN_MultiKernel (class in peptdeep.model.building_block) SeqGRU (class in peptdeep.model.building_block) SeqGRUDecoder (in module peptdeep.model.building_block) SeqLSTM (class in peptdeep.model.building_block) SeqLSTMDecoder (in module peptdeep.model.building_block) SequenceLibraryMaker (class in peptdeep.spec_lib.library_factory) set_bert_trainable() (peptdeep.model.model_interface.ModelInterface method) set_callback_handler() (peptdeep.model.model_interface.ModelInterface method) set_default_nce() (peptdeep.pretrained_models.ModelManager method) set_default_nce_instrument() (peptdeep.pretrained_models.ModelManager method) set_device() (peptdeep.model.model_interface.ModelInterface method) set_layer_trainable() (peptdeep.model.model_interface.ModelInterface method) set_lr() (peptdeep.model.model_interface.ModelInterface method) set_lr_scheduler_class() (peptdeep.model.model_interface.ModelInterface method) set_precursor_and_fragment() (peptdeep.spec_lib.predict_lib.PredictSpecLib method) spearman() (in module peptdeep.model.ms2) spearman_correlation() (in module peptdeep.model.ms2) spectral_angle() (in module peptdeep.model.ms2) step() (peptdeep.model.model_interface.LR_SchedulerInterface method) (peptdeep.model.model_interface.WarmupLR_Scheduler method) supported_charged_frag_types (peptdeep.model.ms2.ModelMS2Bert property) T target_column_to_predict (peptdeep.model.model_interface.ModelInterface property) target_column_to_train (peptdeep.model.model_interface.ModelInterface property) tensor_to_charged_frags() (in module peptdeep.model.ms2) test() (peptdeep.model.ccs.AlphaCCSModel method) (peptdeep.model.ms2.pDeepModel method) (peptdeep.model.rt.AlphaRTModel method) ThermoRawMS1Reader (class in peptdeep.mass_spec.ms_reader) ThermoRawMS2Reader (class in peptdeep.mass_spec.ms_reader) train() (peptdeep.model.model_interface.ModelInterface method) (peptdeep.model.ms2.pDeepModel method) train_ccs_model() (peptdeep.pretrained_models.ModelManager method) train_charge_model() (peptdeep.pretrained_models.ModelManager method) train_ms2_model() (peptdeep.pretrained_models.ModelManager method) train_rt_model() (peptdeep.pretrained_models.ModelManager method) train_with_warmup() (peptdeep.model.model_interface.ModelInterface method) (peptdeep.model.ms2.pDeepModel method) transfer_learn() (in module peptdeep.pipeline_api) translate_library() (peptdeep.spec_lib.library_factory.PredictLibraryMakerBase method) translate_rt_to_irt_pred() (peptdeep.spec_lib.predict_lib.PredictSpecLib method) translate_to_tsv() (peptdeep.spec_lib.library_factory.PredictLibraryMakerBase method) U update_all_mod_features() (in module peptdeep.settings) update_global_settings() (in module peptdeep.settings) update_modifications() (in module peptdeep.settings) update_settings() (in module peptdeep.settings) use_grid_nce_search (peptdeep.pretrained_models.ModelManager attribute) W WarmupLR_Scheduler (class in peptdeep.model.model_interface) X xavier_param() (in module peptdeep.model.building_block) Z zero_param() (in module peptdeep.model.building_block)