# Autogenerated by nbdev

d = { 'settings': { 'branch': 'main',
                'doc_baseurl': '/alphapeptdeep',
                'doc_host': 'https://MannLabs.github.io',
                'git_url': 'https://github.com/MannLabs/alphapeptdeep',
                'lib_path': 'peptdeep'},
  'syms': { 'peptdeep.cli': {},
            'peptdeep.gui': {},
            'peptdeep.legacy.thermo_raw.pyrawfilereader': {},
            'peptdeep.mass_spec.mass_calibration': { 'peptdeep.mass_spec.mass_calibration.MassCalibratorForRT_KNN': ( 'mass_spec/mass_calibration.html#masscalibratorforrt_knn',
                                                                                                                      'peptdeep/mass_spec/mass_calibration.py'),
                                                     'peptdeep.mass_spec.mass_calibration.MassCalibratorForRT_KNN.__init__': ( 'mass_spec/mass_calibration.html#__init__',
                                                                                                                               'peptdeep/mass_spec/mass_calibration.py'),
                                                     'peptdeep.mass_spec.mass_calibration.MassCalibratorForRT_KNN.calibrate': ( 'mass_spec/mass_calibration.html#calibrate',
                                                                                                                                'peptdeep/mass_spec/mass_calibration.py'),
                                                     'peptdeep.mass_spec.mass_calibration.MassCalibratorForRT_KNN.fit': ( 'mass_spec/mass_calibration.html#fit',
                                                                                                                          'peptdeep/mass_spec/mass_calibration.py'),
                                                     'peptdeep.mass_spec.mass_calibration.calibrate_one': ( 'mass_spec/mass_calibration.html#calibrate_one',
                                                                                                            'peptdeep/mass_spec/mass_calibration.py'),
                                                     'peptdeep.mass_spec.mass_calibration.get_fragment_median': ( 'mass_spec/mass_calibration.html#get_fragment_median',
                                                                                                                  'peptdeep/mass_spec/mass_calibration.py')},
            'peptdeep.mass_spec.match': { 'peptdeep.mass_spec.match.PepSpecMatch': ( 'mass_spec/match.html#pepspecmatch',
                                                                                     'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.PepSpecMatch.__init__': ( 'mass_spec/match.html#__init__',
                                                                                              'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.PepSpecMatch._match_ms2_centroid_one_raw': ( 'mass_spec/match.html#_match_ms2_centroid_one_raw',
                                                                                                                 'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.PepSpecMatch._preprocess_psms': ( 'mass_spec/match.html#_preprocess_psms',
                                                                                                      'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.PepSpecMatch.get_fragment_mz_df': ( 'mass_spec/match.html#get_fragment_mz_df',
                                                                                                        'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.PepSpecMatch.match_ms2_centroid': ( 'mass_spec/match.html#match_ms2_centroid',
                                                                                                        'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.PepSpecMatch.match_ms2_one_raw': ( 'mass_spec/match.html#match_ms2_one_raw',
                                                                                                       'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.match_centroid_mz': ( 'mass_spec/match.html#match_centroid_mz',
                                                                                          'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.match_one_raw_with_numba': ( 'mass_spec/match.html#match_one_raw_with_numba',
                                                                                                 'peptdeep/mass_spec/match.py'),
                                          'peptdeep.mass_spec.match.match_profile_mz': ( 'mass_spec/match.html#match_profile_mz',
                                                                                         'peptdeep/mass_spec/match.py')},
            'peptdeep.mass_spec.ms_reader': { 'peptdeep.mass_spec.ms_reader.AlphaPept_HDF_MS1_Reader': ( 'mass_spec/ms_reader.html#alphapept_hdf_ms1_reader',
                                                                                                         'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.AlphaPept_HDF_MS1_Reader.load': ( 'mass_spec/ms_reader.html#load',
                                                                                                              'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.AlphaPept_HDF_MS2_Reader': ( 'mass_spec/ms_reader.html#alphapept_hdf_ms2_reader',
                                                                                                         'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.AlphaPept_HDF_MS2_Reader.load': ( 'mass_spec/ms_reader.html#load',
                                                                                                              'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MGFReader': ( 'mass_spec/ms_reader.html#mgfreader',
                                                                                          'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MGFReader.load': ( 'mass_spec/ms_reader.html#load',
                                                                                               'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderBase': ( 'mass_spec/ms_reader.html#msreaderbase',
                                                                                             'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderBase.__init__': ( 'mass_spec/ms_reader.html#__init__',
                                                                                                      'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderBase.build_spectrum_df': ( 'mass_spec/ms_reader.html#build_spectrum_df',
                                                                                                               'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderBase.get_peaks': ( 'mass_spec/ms_reader.html#get_peaks',
                                                                                                       'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderBase.get_peaks_by_scan_num': ( 'mass_spec/ms_reader.html#get_peaks_by_scan_num',
                                                                                                                   'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderBase.load': ( 'mass_spec/ms_reader.html#load',
                                                                                                  'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderProvider': ( 'mass_spec/ms_reader.html#msreaderprovider',
                                                                                                 'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderProvider.__init__': ( 'mass_spec/ms_reader.html#__init__',
                                                                                                          'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderProvider.get_reader': ( 'mass_spec/ms_reader.html#get_reader',
                                                                                                            'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.MSReaderProvider.register_reader': ( 'mass_spec/ms_reader.html#register_reader',
                                                                                                                 'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.find_line': ( 'mass_spec/ms_reader.html#find_line',
                                                                                          'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.index_ragged_list': ( 'mass_spec/ms_reader.html#index_ragged_list',
                                                                                                  'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.is_pfind_mgf': ( 'mass_spec/ms_reader.html#is_pfind_mgf',
                                                                                             'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.parse_pfind_scan_from_TITLE': ( 'mass_spec/ms_reader.html#parse_pfind_scan_from_title',
                                                                                                            'peptdeep/mass_spec/ms_reader.py'),
                                              'peptdeep.mass_spec.ms_reader.read_until': ( 'mass_spec/ms_reader.html#read_until',
                                                                                           'peptdeep/mass_spec/ms_reader.py')},
            'peptdeep.model.base': {},
            'peptdeep.model.building_block': { 'peptdeep.model.building_block.AA_Mod_Embedding': ( 'model/building_block.html#aa_mod_embedding',
                                                                                                   'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.AA_Mod_Embedding.__init__': ( 'model/building_block.html#__init__',
                                                                                                            'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.AA_Mod_Embedding.forward': ( 'model/building_block.html#forward',
                                                                                                           'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_GRU': ( 'model/building_block.html#decoder_gru',
                                                                                              'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_GRU.__init__': ( 'model/building_block.html#__init__',
                                                                                                       'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_GRU.forward': ( 'model/building_block.html#forward',
                                                                                                      'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_LSTM': ( 'model/building_block.html#decoder_lstm',
                                                                                               'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_LSTM.__init__': ( 'model/building_block.html#__init__',
                                                                                                        'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_LSTM.forward': ( 'model/building_block.html#forward',
                                                                                                       'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_Linear': ( 'model/building_block.html#decoder_linear',
                                                                                                 'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_Linear.__init__': ( 'model/building_block.html#__init__',
                                                                                                          'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Decoder_Linear.forward': ( 'model/building_block.html#forward',
                                                                                                         'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM': ( 'model/building_block.html#encoder_26aa_mod_cnn_lstm',
                                                                                                            'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM.__init__': ( 'model/building_block.html#__init__',
                                                                                                                     'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM.forward': ( 'model/building_block.html#forward',
                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM_AttnSum': ( 'model/building_block.html#encoder_26aa_mod_cnn_lstm_attnsum',
                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM_AttnSum.__init__': ( 'model/building_block.html#__init__',
                                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_CNN_LSTM_AttnSum.forward': ( 'model/building_block.html#forward',
                                                                                                                            'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_Charge_CNN_LSTM_AttnSum': ( 'model/building_block.html#encoder_26aa_mod_charge_cnn_lstm_attnsum',
                                                                                                                           'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_Charge_CNN_LSTM_AttnSum.__init__': ( 'model/building_block.html#__init__',
                                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_Charge_CNN_LSTM_AttnSum.forward': ( 'model/building_block.html#forward',
                                                                                                                                   'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_LSTM': ( 'model/building_block.html#encoder_26aa_mod_lstm',
                                                                                                        'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_LSTM.__init__': ( 'model/building_block.html#__init__',
                                                                                                                 'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_26AA_Mod_LSTM.forward': ( 'model/building_block.html#forward',
                                                                                                                'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_CNN_LSTM_AttnSum': ( 'model/building_block.html#encoder_aa_mod_cnn_lstm_attnsum',
                                                                                                                  'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_CNN_LSTM_AttnSum.__init__': ( 'model/building_block.html#__init__',
                                                                                                                           'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_CNN_LSTM_AttnSum.forward': ( 'model/building_block.html#forward',
                                                                                                                          'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer': ( 'model/building_block.html#encoder_aa_mod_charge_transformer',
                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer.__init__': ( 'model/building_block.html#__init__',
                                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer.forward': ( 'model/building_block.html#forward',
                                                                                                                            'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer_AttnSum': ( 'model/building_block.html#encoder_aa_mod_charge_transformer_attnsum',
                                                                                                                            'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer_AttnSum.__init__': ( 'model/building_block.html#__init__',
                                                                                                                                     'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Charge_Transformer_AttnSum.forward': ( 'model/building_block.html#forward',
                                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Transformer': ( 'model/building_block.html#encoder_aa_mod_transformer',
                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Transformer.__init__': ( 'model/building_block.html#__init__',
                                                                                                                      'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Transformer.forward': ( 'model/building_block.html#forward',
                                                                                                                     'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Transformer_AttnSum': ( 'model/building_block.html#encoder_aa_mod_transformer_attnsum',
                                                                                                                     'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Transformer_AttnSum.__init__': ( 'model/building_block.html#__init__',
                                                                                                                              'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Encoder_AA_Mod_Transformer_AttnSum.forward': ( 'model/building_block.html#forward',
                                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.HFace_Transformer_with_PositionalEncoder': ( 'model/building_block.html#hface_transformer_with_positionalencoder',
                                                                                                                           'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.HFace_Transformer_with_PositionalEncoder.__init__': ( 'model/building_block.html#__init__',
                                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.HFace_Transformer_with_PositionalEncoder.forward': ( 'model/building_block.html#forward',
                                                                                                                                   'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Hidden_HFace_Transformer': ( 'model/building_block.html#hidden_hface_transformer',
                                                                                                           'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Hidden_HFace_Transformer.__init__': ( 'model/building_block.html#__init__',
                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Hidden_HFace_Transformer.forward': ( 'model/building_block.html#forward',
                                                                                                                   'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Hidden_Transformer': ( 'model/building_block.html#hidden_transformer',
                                                                                                     'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Hidden_Transformer.__init__': ( 'model/building_block.html#__init__',
                                                                                                              'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Hidden_Transformer.forward': ( 'model/building_block.html#forward',
                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_Charge_LSTM': ( 'model/building_block.html#input_26aa_mod_charge_lstm',
                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_Charge_LSTM.__init__': ( 'model/building_block.html#__init__',
                                                                                                                      'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_Charge_LSTM.forward': ( 'model/building_block.html#forward',
                                                                                                                     'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_LSTM': ( 'model/building_block.html#input_26aa_mod_lstm',
                                                                                                      'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_LSTM.__init__': ( 'model/building_block.html#__init__',
                                                                                                               'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_LSTM.forward': ( 'model/building_block.html#forward',
                                                                                                              'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_Meta_LSTM': ( 'model/building_block.html#input_26aa_mod_meta_lstm',
                                                                                                           'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_Meta_LSTM.__init__': ( 'model/building_block.html#__init__',
                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_Meta_LSTM.forward': ( 'model/building_block.html#forward',
                                                                                                                   'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_PositionalEncoding': ( 'model/building_block.html#input_26aa_mod_positionalencoding',
                                                                                                                    'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_PositionalEncoding.__init__': ( 'model/building_block.html#__init__',
                                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_26AA_Mod_PositionalEncoding.forward': ( 'model/building_block.html#forward',
                                                                                                                            'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_AA_Mod_Charge_PositionalEncoding': ( 'model/building_block.html#input_aa_mod_charge_positionalencoding',
                                                                                                                         'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_AA_Mod_Charge_PositionalEncoding.__init__': ( 'model/building_block.html#__init__',
                                                                                                                                  'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_AA_Mod_Charge_PositionalEncoding.forward': ( 'model/building_block.html#forward',
                                                                                                                                 'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_AA_Mod_PositionalEncoding': ( 'model/building_block.html#input_aa_mod_positionalencoding',
                                                                                                                  'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_AA_Mod_PositionalEncoding.__init__': ( 'model/building_block.html#__init__',
                                                                                                                           'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Input_AA_Mod_PositionalEncoding.forward': ( 'model/building_block.html#forward',
                                                                                                                          'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Meta_Embedding': ( 'model/building_block.html#meta_embedding',
                                                                                                 'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Meta_Embedding.__init__': ( 'model/building_block.html#__init__',
                                                                                                          'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Meta_Embedding.forward': ( 'model/building_block.html#forward',
                                                                                                         'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Mod_Embedding': ( 'model/building_block.html#mod_embedding',
                                                                                                'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Mod_Embedding.__init__': ( 'model/building_block.html#__init__',
                                                                                                         'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Mod_Embedding.forward': ( 'model/building_block.html#forward',
                                                                                                        'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Mod_Embedding_FixFirstK': ( 'model/building_block.html#mod_embedding_fixfirstk',
                                                                                                          'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Mod_Embedding_FixFirstK.__init__': ( 'model/building_block.html#__init__',
                                                                                                                   'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.Mod_Embedding_FixFirstK.forward': ( 'model/building_block.html#forward',
                                                                                                                  'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.PositionalEmbedding': ( 'model/building_block.html#positionalembedding',
                                                                                                      'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.PositionalEmbedding.__init__': ( 'model/building_block.html#__init__',
                                                                                                               'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.PositionalEmbedding.forward': ( 'model/building_block.html#forward',
                                                                                                              'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.PositionalEncoding': ( 'model/building_block.html#positionalencoding',
                                                                                                     'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.PositionalEncoding.__init__': ( 'model/building_block.html#__init__',
                                                                                                              'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.PositionalEncoding.forward': ( 'model/building_block.html#forward',
                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqAttentionSum': ( 'model/building_block.html#seqattentionsum',
                                                                                                  'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqAttentionSum.__init__': ( 'model/building_block.html#__init__',
                                                                                                           'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqAttentionSum.forward': ( 'model/building_block.html#forward',
                                                                                                          'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqCNN': ( 'model/building_block.html#seqcnn',
                                                                                         'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqCNN.__init__': ( 'model/building_block.html#__init__',
                                                                                                  'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqCNN.forward': ( 'model/building_block.html#forward',
                                                                                                 'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqCNN_MultiKernel': ( 'model/building_block.html#seqcnn_multikernel',
                                                                                                     'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqCNN_MultiKernel.__init__': ( 'model/building_block.html#__init__',
                                                                                                              'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqCNN_MultiKernel.forward': ( 'model/building_block.html#forward',
                                                                                                             'peptdeep/model/building_block.py'),
                                               'peptdeep.model.building_block.SeqGRU': ( 'model/building_block.html#seqgru',
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                                    'peptdeep.model.ms2.IntenAwareLoss.forward': ('model/ms2.html#forward', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2Bert': ('model/ms2.html#modelms2bert', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2Bert.__init__': ('model/ms2.html#__init__', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2Bert.forward': ('model/ms2.html#forward', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2Bert.output_attentions': ( 'model/ms2.html#output_attentions',
                                                                                           'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2Transformer': ( 'model/ms2.html#modelms2transformer',
                                                                                'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2Transformer.__init__': ('model/ms2.html#__init__', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2Transformer.forward': ('model/ms2.html#forward', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2pDeep': ('model/ms2.html#modelms2pdeep', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2pDeep.__init__': ('model/ms2.html#__init__', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.ModelMS2pDeep.forward': ('model/ms2.html#forward', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2._get_ranks': ('model/ms2.html#_get_ranks', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.add_cutoff_metric': ('model/ms2.html#add_cutoff_metric', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.calc_ms2_similarity': ( 'model/ms2.html#calc_ms2_similarity',
                                                                                'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.normalize_fragment_intensities_': ( 'model/ms2.html#normalize_fragment_intensities_',
                                                                                            'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.normalize_training_intensities': ( 'model/ms2.html#normalize_training_intensities',
                                                                                           'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel': ('model/ms2.html#pdeepmodel', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel.__init__': ('model/ms2.html#__init__', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel._check_predict_in_order': ( 'model/ms2.html#_check_predict_in_order',
                                                                                               'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel._get_features_from_batch_df': ( 'model/ms2.html#_get_features_from_batch_df',
                                                                                                   'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel._get_modloss_frags': ( 'model/ms2.html#_get_modloss_frags',
                                                                                          'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel._get_targets_from_batch_df': ( 'model/ms2.html#_get_targets_from_batch_df',
                                                                                                  'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel._prepare_predict_data_df': ( 'model/ms2.html#_prepare_predict_data_df',
                                                                                                'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel._prepare_train_data_df': ( 'model/ms2.html#_prepare_train_data_df',
                                                                                              'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel._set_batch_predict_data': ( 'model/ms2.html#_set_batch_predict_data',
                                                                                               'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel.bootstrap_nce_search': ( 'model/ms2.html#bootstrap_nce_search',
                                                                                            'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel.grid_nce_search': ( 'model/ms2.html#grid_nce_search',
                                                                                       'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel.predict': ('model/ms2.html#predict', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel.predict_mp': ('model/ms2.html#predict_mp', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel.train': ('model/ms2.html#train', 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pDeepModel.train_with_warmup': ( 'model/ms2.html#train_with_warmup',
                                                                                         'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.pearson_correlation': ( 'model/ms2.html#pearson_correlation',
                                                                                'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.spearman_correlation': ( 'model/ms2.html#spearman_correlation',
                                                                                 'peptdeep/model/ms2.py'),
                                    'peptdeep.model.ms2.spectral_angle': ('model/ms2.html#spectral_angle', 'peptdeep/model/ms2.py')},
            'peptdeep.model.rt': { 'peptdeep.model.rt.AlphaRTModel': ('model/rt.html#alphartmodel', 'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.AlphaRTModel.__init__': ('model/rt.html#__init__', 'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.AlphaRTModel._get_features_from_batch_df': ( 'model/rt.html#_get_features_from_batch_df',
                                                                                                   'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.AlphaRTModel.add_irt_column_to_precursor_df': ( 'model/rt.html#add_irt_column_to_precursor_df',
                                                                                                      'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.Model_RT_Bert': ('model/rt.html#model_rt_bert', 'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.Model_RT_Bert.__init__': ('model/rt.html#__init__', 'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.Model_RT_Bert.forward': ('model/rt.html#forward', 'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.Model_RT_Bert.output_attentions': ( 'model/rt.html#output_attentions',
                                                                                          'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.Model_RT_LSTM_CNN': ('model/rt.html#model_rt_lstm_cnn', 'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.Model_RT_LSTM_CNN.__init__': ('model/rt.html#__init__', 'peptdeep/model/rt.py'),
                                   'peptdeep.model.rt.Model_RT_LSTM_CNN.forward': ('model/rt.html#forward', 'peptdeep/model/rt.py')},
            'peptdeep.pipeline_api': { 'peptdeep.pipeline_api._get_delimiter': ( 'pipeline_api.html#_get_delimiter',
                                                                                 'peptdeep/pipeline_api.py'),
                                       'peptdeep.pipeline_api.generate_library': ( 'pipeline_api.html#generate_library',
                                                                                   'peptdeep/pipeline_api.py'),
                                       'peptdeep.pipeline_api.import_psm_df': ( 'pipeline_api.html#import_psm_df',
                                                                                'peptdeep/pipeline_api.py'),
                                       'peptdeep.pipeline_api.load_settings': ( 'pipeline_api.html#load_settings',
                                                                                'peptdeep/pipeline_api.py'),
                                       'peptdeep.pipeline_api.match_psms': ('pipeline_api.html#match_psms', 'peptdeep/pipeline_api.py'),
                                       'peptdeep.pipeline_api.rescore': ('pipeline_api.html#rescore', 'peptdeep/pipeline_api.py'),
                                       'peptdeep.pipeline_api.transfer_learn': ( 'pipeline_api.html#transfer_learn',
                                                                                 'peptdeep/pipeline_api.py')},
            'peptdeep.pretrained_models': { 'peptdeep.pretrained_models.ModelManager': ( 'pretrained_models.html#modelmanager',
                                                                                         'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.__init__': ( 'pretrained_models.html#__init__',
                                                                                                  'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager._predict_all_for_mp': ( 'pretrained_models.html#_predict_all_for_mp',
                                                                                                             'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.instrument': ( 'pretrained_models.html#instrument',
                                                                                                    'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.load_external_models': ( 'pretrained_models.html#load_external_models',
                                                                                                              'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.load_installed_models': ( 'pretrained_models.html#load_installed_models',
                                                                                                               'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.predict_all': ( 'pretrained_models.html#predict_all',
                                                                                                     'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.predict_mobility': ( 'pretrained_models.html#predict_mobility',
                                                                                                          'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.predict_ms2': ( 'pretrained_models.html#predict_ms2',
                                                                                                     'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.predict_rt': ( 'pretrained_models.html#predict_rt',
                                                                                                    'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.set_default_nce': ( 'pretrained_models.html#set_default_nce',
                                                                                                         'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.set_default_nce_instrument': ( 'pretrained_models.html#set_default_nce_instrument',
                                                                                                                    'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.train_ccs_model': ( 'pretrained_models.html#train_ccs_model',
                                                                                                         'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.train_ms2_model': ( 'pretrained_models.html#train_ms2_model',
                                                                                                         'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.ModelManager.train_rt_model': ( 'pretrained_models.html#train_rt_model',
                                                                                                        'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.clear_error_modloss_intensities': ( 'pretrained_models.html#clear_error_modloss_intensities',
                                                                                                            'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.count_mods': ( 'pretrained_models.html#count_mods',
                                                                                       'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.download_models': ( 'pretrained_models.html#download_models',
                                                                                            'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.is_model_zip': ( 'pretrained_models.html#is_model_zip',
                                                                                         'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.load_models': ( 'pretrained_models.html#load_models',
                                                                                        'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.load_models_by_model_type_in_zip': ( 'pretrained_models.html#load_models_by_model_type_in_zip',
                                                                                                             'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.load_phos_models': ( 'pretrained_models.html#load_phos_models',
                                                                                             'peptdeep/pretrained_models.py'),
                                            'peptdeep.pretrained_models.psm_sampling_with_important_mods': ( 'pretrained_models.html#psm_sampling_with_important_mods',
                                                                                                             'peptdeep/pretrained_models.py')},
            'peptdeep.protein.fasta': { 'peptdeep.protein.fasta.PredictFastaSpecLib': ( 'protein/fasta.html#predictfastaspeclib',
                                                                                        'peptdeep/protein/fasta.py'),
                                        'peptdeep.protein.fasta.PredictFastaSpecLib.__init__': ( 'protein/fasta.html#__init__',
                                                                                                 'peptdeep/protein/fasta.py'),
                                        'peptdeep.protein.fasta.PredictFastaSpecLib._process_after_load_pep_seqs': ( 'protein/fasta.html#_process_after_load_pep_seqs',
                                                                                                                     'peptdeep/protein/fasta.py')},
            'peptdeep.psm_frag_reader.library_frag_reader': { 'peptdeep.psm_frag_reader.library_frag_reader.SpectronautMSMSReader': ( 'psm_frag_reader/library_frag_reader.html#spectronautmsmsreader',
                                                                                                                                      'peptdeep/psm_frag_reader/library_frag_reader.py'),
                                                              'peptdeep.psm_frag_reader.library_frag_reader.SpectronautMSMSReader.__init__': ( 'psm_frag_reader/library_frag_reader.html#__init__',
                                                                                                                                               'peptdeep/psm_frag_reader/library_frag_reader.py'),
                                                              'peptdeep.psm_frag_reader.library_frag_reader.SpectronautMSMSReader._find_mapped_columns': ( 'psm_frag_reader/library_frag_reader.html#_find_mapped_columns',
                                                                                                                                                           'peptdeep/psm_frag_reader/library_frag_reader.py'),
                                                              'peptdeep.psm_frag_reader.library_frag_reader.SpectronautMSMSReader._get_fragment_intensity': ( 'psm_frag_reader/library_frag_reader.html#_get_fragment_intensity',
                                                                                                                                                              'peptdeep/psm_frag_reader/library_frag_reader.py'),
                                                              'peptdeep.psm_frag_reader.library_frag_reader.SpectronautMSMSReader._load_file': ( 'psm_frag_reader/library_frag_reader.html#_load_file',
                                                                                                                                                 'peptdeep/psm_frag_reader/library_frag_reader.py'),
                                                              'peptdeep.psm_frag_reader.library_frag_reader.SpectronautMSMSReader._post_process': ( 'psm_frag_reader/library_frag_reader.html#_post_process',
                                                                                                                                                    'peptdeep/psm_frag_reader/library_frag_reader.py'),
                                                              'peptdeep.psm_frag_reader.library_frag_reader.SpectronautMSMSReader.fragment_intensity_df': ( 'psm_frag_reader/library_frag_reader.html#fragment_intensity_df',
                                                                                                                                                            'peptdeep/psm_frag_reader/library_frag_reader.py')},
            'peptdeep.psm_frag_reader.maxquant_frag_reader': { 'peptdeep.psm_frag_reader.maxquant_frag_reader.MaxQuantMSMSReader': ( 'psm_frag_reader/maxquant_frag_reader.html#maxquantmsmsreader',
                                                                                                                                     'peptdeep/psm_frag_reader/maxquant_frag_reader.py'),
                                                               'peptdeep.psm_frag_reader.maxquant_frag_reader.MaxQuantMSMSReader.__init__': ( 'psm_frag_reader/maxquant_frag_reader.html#__init__',
                                                                                                                                              'peptdeep/psm_frag_reader/maxquant_frag_reader.py'),
                                                               'peptdeep.psm_frag_reader.maxquant_frag_reader.MaxQuantMSMSReader._load_file': ( 'psm_frag_reader/maxquant_frag_reader.html#_load_file',
                                                                                                                                                'peptdeep/psm_frag_reader/maxquant_frag_reader.py'),
                                                               'peptdeep.psm_frag_reader.maxquant_frag_reader.MaxQuantMSMSReader._post_process': ( 'psm_frag_reader/maxquant_frag_reader.html#_post_process',
                                                                                                                                                   'peptdeep/psm_frag_reader/maxquant_frag_reader.py'),
                                                               'peptdeep.psm_frag_reader.maxquant_frag_reader.MaxQuantMSMSReader.fragment_intensity_df': ( 'psm_frag_reader/maxquant_frag_reader.html#fragment_intensity_df',
                                                                                                                                                           'peptdeep/psm_frag_reader/maxquant_frag_reader.py'),
                                                               'peptdeep.psm_frag_reader.maxquant_frag_reader.filter_phos': ( 'psm_frag_reader/maxquant_frag_reader.html#filter_phos',
                                                                                                                              'peptdeep/psm_frag_reader/maxquant_frag_reader.py'),
                                                               'peptdeep.psm_frag_reader.maxquant_frag_reader.parse_phos_probs': ( 'psm_frag_reader/maxquant_frag_reader.html#parse_phos_probs',
                                                                                                                                   'peptdeep/psm_frag_reader/maxquant_frag_reader.py')},
            'peptdeep.psm_frag_reader.psm_frag_reader': { 'peptdeep.psm_frag_reader.psm_frag_reader.PSMReader_w_FragBase': ( 'psm_frag_reader/psm_frag_reader.html#psmreader_w_fragbase',
                                                                                                                             'peptdeep/psm_frag_reader/psm_frag_reader.py'),
                                                          'peptdeep.psm_frag_reader.psm_frag_reader.PSMReader_w_FragBase.__init__': ( 'psm_frag_reader/psm_frag_reader.html#__init__',
                                                                                                                                      'peptdeep/psm_frag_reader/psm_frag_reader.py'),
                                                          'peptdeep.psm_frag_reader.psm_frag_reader.PSMReader_w_FragBase.fragment_intensity_df': ( 'psm_frag_reader/psm_frag_reader.html#fragment_intensity_df',
                                                                                                                                                   'peptdeep/psm_frag_reader/psm_frag_reader.py'),
                                                          'peptdeep.psm_frag_reader.psm_frag_reader.PSM_w_FragReaderProvider': ( 'psm_frag_reader/psm_frag_reader.html#psm_w_fragreaderprovider',
                                                                                                                                 'peptdeep/psm_frag_reader/psm_frag_reader.py'),
                                                          'peptdeep.psm_frag_reader.psm_frag_reader.PSM_w_FragReaderProvider.__init__': ( 'psm_frag_reader/psm_frag_reader.html#__init__',
                                                                                                                                          'peptdeep/psm_frag_reader/psm_frag_reader.py'),
                                                          'peptdeep.psm_frag_reader.psm_frag_reader.PSM_w_FragReaderProvider.get_reader': ( 'psm_frag_reader/psm_frag_reader.html#get_reader',
                                                                                                                                            'peptdeep/psm_frag_reader/psm_frag_reader.py'),
                                                          'peptdeep.psm_frag_reader.psm_frag_reader.PSM_w_FragReaderProvider.register_reader': ( 'psm_frag_reader/psm_frag_reader.html#register_reader',
                                                                                                                                                 'peptdeep/psm_frag_reader/psm_frag_reader.py')},
            'peptdeep.psm_frag_reader.psmlabel_reader': { 'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader': ( 'psm_frag_reader/psmlabel_reader.html#psmlabelreader',
                                                                                                                       'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader.__init__': ( 'psm_frag_reader/psmlabel_reader.html#__init__',
                                                                                                                                'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader._init_column_mapping': ( 'psm_frag_reader/psmlabel_reader.html#_init_column_mapping',
                                                                                                                                            'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader._load_file': ( 'psm_frag_reader/psmlabel_reader.html#_load_file',
                                                                                                                                  'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader._load_modifications': ( 'psm_frag_reader/psmlabel_reader.html#_load_modifications',
                                                                                                                                           'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader._post_process': ( 'psm_frag_reader/psmlabel_reader.html#_post_process',
                                                                                                                                     'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader._translate_decoy': ( 'psm_frag_reader/psmlabel_reader.html#_translate_decoy',
                                                                                                                                        'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader._translate_modifications': ( 'psm_frag_reader/psmlabel_reader.html#_translate_modifications',
                                                                                                                                                'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.PSMLabelReader._translate_score': ( 'psm_frag_reader/psmlabel_reader.html#_translate_score',
                                                                                                                                        'peptdeep/psm_frag_reader/psmlabel_reader.py'),
                                                          'peptdeep.psm_frag_reader.psmlabel_reader.load_psmlabel_list': ( 'psm_frag_reader/psmlabel_reader.html#load_psmlabel_list',
                                                                                                                           'peptdeep/psm_frag_reader/psmlabel_reader.py')},
            'peptdeep.rescore.fdr': { 'peptdeep.rescore.fdr.calc_fdr': ('rescore/fdr.html#calc_fdr', 'peptdeep/rescore/fdr.py'),
                                      'peptdeep.rescore.fdr.calc_fdr_from_ref': ( 'rescore/fdr.html#calc_fdr_from_ref',
                                                                                  'peptdeep/rescore/fdr.py'),
                                      'peptdeep.rescore.fdr.fdr_from_ref': ('rescore/fdr.html#fdr_from_ref', 'peptdeep/rescore/fdr.py'),
                                      'peptdeep.rescore.fdr.fdr_to_q_values': ( 'rescore/fdr.html#fdr_to_q_values',
                                                                                'peptdeep/rescore/fdr.py')},
            'peptdeep.rescore.feature_extractor': { 'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor': ( 'rescore/feature_extractor.html#scorefeatureextractor',
                                                                                                                  'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor.__init__': ( 'rescore/feature_extractor.html#__init__',
                                                                                                                           'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor._get_model_frag_types': ( 'rescore/feature_extractor.html#_get_model_frag_types',
                                                                                                                                        'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor._select_raw_to_tune': ( 'rescore/feature_extractor.html#_select_raw_to_tune',
                                                                                                                                      'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor._tune': ( 'rescore/feature_extractor.html#_tune',
                                                                                                                        'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor.extract_features': ( 'rescore/feature_extractor.html#extract_features',
                                                                                                                                   'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor.extract_mobility_features': ( 'rescore/feature_extractor.html#extract_mobility_features',
                                                                                                                                            'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor.extract_rt_features': ( 'rescore/feature_extractor.html#extract_rt_features',
                                                                                                                                      'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor.fine_tune_models': ( 'rescore/feature_extractor.html#fine_tune_models',
                                                                                                                                   'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractor.match_ms2': ( 'rescore/feature_extractor.html#match_ms2',
                                                                                                                            'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP': ( 'rescore/feature_extractor.html#scorefeatureextractormp',
                                                                                                                    'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP.__init__': ( 'rescore/feature_extractor.html#__init__',
                                                                                                                             'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP.extract_features': ( 'rescore/feature_extractor.html#extract_features',
                                                                                                                                     'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP.extract_features_one_raw': ( 'rescore/feature_extractor.html#extract_features_one_raw',
                                                                                                                                             'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.ScoreFeatureExtractorMP.fine_tune_models': ( 'rescore/feature_extractor.html#fine_tune_models',
                                                                                                                                     'peptdeep/rescore/feature_extractor.py'),
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                                                                                                             'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.get_ms2_features_mp': ( 'rescore/feature_extractor.html#get_ms2_features_mp',
                                                                                                                'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.get_psm_scores': ( 'rescore/feature_extractor.html#get_psm_scores',
                                                                                                           'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.match_one_raw': ( 'rescore/feature_extractor.html#match_one_raw',
                                                                                                          'peptdeep/rescore/feature_extractor.py'),
                                                    'peptdeep.rescore.feature_extractor.match_one_raw_mp': ( 'rescore/feature_extractor.html#match_one_raw_mp',
                                                                                                             'peptdeep/rescore/feature_extractor.py')},
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                                                                                                      'peptdeep/rescore/percolator.py'),
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                                                                                                               'peptdeep/rescore/percolator.py'),
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                                                                                                              'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.NNRescore': ( 'rescore/percolator.html#nnrescore',
                                                                                        'peptdeep/rescore/percolator.py'),
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                                                                                                 'peptdeep/rescore/percolator.py'),
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                                                                                                          'peptdeep/rescore/percolator.py'),
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                                                                                            'peptdeep/rescore/percolator.py'),
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                                                                                         'peptdeep/rescore/percolator.py'),
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                                                                                                  'peptdeep/rescore/percolator.py'),
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                                                                                                   'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.Percolator._estimate_fdr': ( 'rescore/percolator.html#_estimate_fdr',
                                                                                                       'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.Percolator._predict': ( 'rescore/percolator.html#_predict',
                                                                                                  'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.Percolator._train': ( 'rescore/percolator.html#_train',
                                                                                                'peptdeep/rescore/percolator.py'),
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                                                                                                                  'peptdeep/rescore/percolator.py'),
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                                                                                                          'peptdeep/rescore/percolator.py'),
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                                                                                                               'peptdeep/rescore/percolator.py'),
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                                                                                                   'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.Percolator.re_score': ( 'rescore/percolator.html#re_score',
                                                                                                  'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.Percolator.run': ( 'rescore/percolator.html#run',
                                                                                             'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.RescoreModelProvider': ( 'rescore/percolator.html#rescoremodelprovider',
                                                                                                   'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.RescoreModelProvider.__init__': ( 'rescore/percolator.html#__init__',
                                                                                                            'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.RescoreModelProvider.get_model': ( 'rescore/percolator.html#get_model',
                                                                                                             'peptdeep/rescore/percolator.py'),
                                             'peptdeep.rescore.percolator.RescoreModelProvider.register': ( 'rescore/percolator.html#register',
                                                                                                            'peptdeep/rescore/percolator.py')},
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                                   'peptdeep.settings.update_settings': ('settings.html#update_settings', 'peptdeep/settings.py')},
            'peptdeep.spec_lib.library_factory': { 'peptdeep.spec_lib.library_factory.FastaLibraryMaker': ( 'spec_lib/library_factory.html#fastalibrarymaker',
                                                                                                            'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.FastaLibraryMaker._input': ( 'spec_lib/library_factory.html#_input',
                                                                                                                   'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.LibraryMakerProvider': ( 'spec_lib/library_factory.html#librarymakerprovider',
                                                                                                               'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.LibraryMakerProvider.__init__': ( 'spec_lib/library_factory.html#__init__',
                                                                                                                        'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.LibraryMakerProvider.get_maker': ( 'spec_lib/library_factory.html#get_maker',
                                                                                                                         'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.LibraryMakerProvider.register_maker': ( 'spec_lib/library_factory.html#register_maker',
                                                                                                                              'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PeptideLibraryMaker': ( 'spec_lib/library_factory.html#peptidelibrarymaker',
                                                                                                              'peptdeep/spec_lib/library_factory.py'),
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                                                                                                                     'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PrecursorLibraryMaker': ( 'spec_lib/library_factory.html#precursorlibrarymaker',
                                                                                                                'peptdeep/spec_lib/library_factory.py'),
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                                                                                                                          'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PrecursorLibraryMaker._input': ( 'spec_lib/library_factory.html#_input',
                                                                                                                       'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase': ( 'spec_lib/library_factory.html#predictlibrarymakerbase',
                                                                                                                  'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase.__init__': ( 'spec_lib/library_factory.html#__init__',
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                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase._check_df': ( 'spec_lib/library_factory.html#_check_df',
                                                                                                                            'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase._input': ( 'spec_lib/library_factory.html#_input',
                                                                                                                         'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase._predict': ( 'spec_lib/library_factory.html#_predict',
                                                                                                                           'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase._set_df': ( 'spec_lib/library_factory.html#_set_df',
                                                                                                                          'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase.make_library': ( 'spec_lib/library_factory.html#make_library',
                                                                                                                               'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase.translate_library': ( 'spec_lib/library_factory.html#translate_library',
                                                                                                                                    'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.PredictLibraryMakerBase.translate_to_tsv': ( 'spec_lib/library_factory.html#translate_to_tsv',
                                                                                                                                   'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.SequenceLibraryMaker': ( 'spec_lib/library_factory.html#sequencelibrarymaker',
                                                                                                               'peptdeep/spec_lib/library_factory.py'),
                                                   'peptdeep.spec_lib.library_factory.SequenceLibraryMaker._input': ( 'spec_lib/library_factory.html#_input',
                                                                                                                      'peptdeep/spec_lib/library_factory.py')},
            'peptdeep.spec_lib.predict_lib': { 'peptdeep.spec_lib.predict_lib.PredictSpecLib': ( 'spec_lib/predict_lib.html#predictspeclib',
                                                                                                 'peptdeep/spec_lib/predict_lib.py'),
                                               'peptdeep.spec_lib.predict_lib.PredictSpecLib.__init__': ( 'spec_lib/predict_lib.html#__init__',
                                                                                                          'peptdeep/spec_lib/predict_lib.py'),
                                               'peptdeep.spec_lib.predict_lib.PredictSpecLib.predict_all': ( 'spec_lib/predict_lib.html#predict_all',
                                                                                                             'peptdeep/spec_lib/predict_lib.py'),
                                               'peptdeep.spec_lib.predict_lib.PredictSpecLib.rt_to_irt_pred': ( 'spec_lib/predict_lib.html#rt_to_irt_pred',
                                                                                                                'peptdeep/spec_lib/predict_lib.py'),
                                               'peptdeep.spec_lib.predict_lib.PredictSpecLib.set_precursor_and_fragment': ( 'spec_lib/predict_lib.html#set_precursor_and_fragment',
                                                                                                                            'peptdeep/spec_lib/predict_lib.py')},
            'peptdeep.spec_lib.translate': { 'peptdeep.spec_lib.translate.WritingProcess': ( 'spec_lib/translate.html#writingprocess',
                                                                                             'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.WritingProcess.__init__': ( 'spec_lib/translate.html#__init__',
                                                                                                      'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.WritingProcess.run': ( 'spec_lib/translate.html#run',
                                                                                                 'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate._get_frag_info_from_column_name': ( 'spec_lib/translate.html#_get_frag_info_from_column_name',
                                                                                                              'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate._get_frag_num': ( 'spec_lib/translate.html#_get_frag_num',
                                                                                            'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.create_modified_sequence': ( 'spec_lib/translate.html#create_modified_sequence',
                                                                                                       'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.is_nterm_frag': ( 'spec_lib/translate.html#is_nterm_frag',
                                                                                            'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.mask_fragment_intensity_by_frag_nAA': ( 'spec_lib/translate.html#mask_fragment_intensity_by_frag_naa',
                                                                                                                  'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.mask_fragment_intensity_by_mz_': ( 'spec_lib/translate.html#mask_fragment_intensity_by_mz_',
                                                                                                             'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.merge_precursor_fragment_df': ( 'spec_lib/translate.html#merge_precursor_fragment_df',
                                                                                                          'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.speclib_to_single_df': ( 'spec_lib/translate.html#speclib_to_single_df',
                                                                                                   'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.speclib_to_swath_df': ( 'spec_lib/translate.html#speclib_to_swath_df',
                                                                                                  'peptdeep/spec_lib/translate.py'),
                                             'peptdeep.spec_lib.translate.translate_to_tsv': ( 'spec_lib/translate.html#translate_to_tsv',
                                                                                               'peptdeep/spec_lib/translate.py')},
            'peptdeep.utils': { 'peptdeep.utils._flatten': ('utils.html#_flatten', 'peptdeep/utils.py'),
                                'peptdeep.utils._is_mps_available': ('utils.html#_is_mps_available', 'peptdeep/utils.py'),
                                'peptdeep.utils.evaluate_linear_regression': ('utils.html#evaluate_linear_regression', 'peptdeep/utils.py'),
                                'peptdeep.utils.evaluate_linear_regression_plot': ( 'utils.html#evaluate_linear_regression_plot',
                                                                                    'peptdeep/utils.py'),
                                'peptdeep.utils.explode_multiple_columns': ('utils.html#explode_multiple_columns', 'peptdeep/utils.py'),
                                'peptdeep.utils.parse_ms_file_names_to_dict': ( 'utils.html#parse_ms_file_names_to_dict',
                                                                                'peptdeep/utils.py'),
                                'peptdeep.utils.process_bar': ('utils.html#process_bar', 'peptdeep/utils.py'),
                                'peptdeep.utils.regional_sampling': ('utils.html#regional_sampling', 'peptdeep/utils.py'),
                                'peptdeep.utils.set_logger': ('utils.html#set_logger', 'peptdeep/utils.py'),
                                'peptdeep.utils.show_platform_info': ('utils.html#show_platform_info', 'peptdeep/utils.py'),
                                'peptdeep.utils.show_python_info': ('utils.html#show_python_info', 'peptdeep/utils.py')},
            'peptdeep.webui.library_ui': {},
            'peptdeep.webui.main_ui': {},
            'peptdeep.webui.model_ui': {},
            'peptdeep.webui.rescore_ui': {},
            'peptdeep.webui.server': {},
            'peptdeep.webui.server_ui': {},
            'peptdeep.webui.settings_ui': {},
            'peptdeep.webui.startpage': {},
            'peptdeep.webui.transfer_ui': {},
            'peptdeep.webui.ui_utils': {}}}