Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z _ __init__() (alphabase.constants.atom.ChemicalCompositonFormula method) (alphabase.constants.isotope.IsotopeDistribution method) (alphabase.io.hdf.HDF_Dataset method) (alphabase.io.hdf.HDF_File method) (alphabase.io.hdf.HDF_Group method) (alphabase.io.hdf.HDF_Object method) (alphabase.peptide.fragment.FragmentType method) (alphabase.pg_reader.alphapept_pg_reader.AlphaPeptPGReader method) (alphabase.pg_reader.fragpipe_pg_reader.FragPipePGReader method) (alphabase.pg_reader.maxquant_pg_reader.MaxQuantPGReader method) (alphabase.pg_reader.mztab_pg_reader.MZTabPGReader method) (alphabase.pg_reader.pg_reader.PGReaderBase method) (alphabase.pg_reader.pg_reader.PGReaderProvider method) (alphabase.pg_reader.spectronaut_reader.SpectronautPGReader method) (alphabase.protein.fasta.Digest method) (alphabase.protein.fasta.SpecLibFasta method) (alphabase.protein.protein_level_decoy.ProteinReverseDecoy method) (alphabase.psm_reader.dia_psm_reader.DiannReader method) (alphabase.psm_reader.maxquant_reader.MaxQuantReader method) (alphabase.psm_reader.maxquant_reader.ModifiedSequenceReader method) (alphabase.psm_reader.msfragger_reader.MSFraggerModificationTranslator method) (alphabase.psm_reader.msfragger_reader.MSFraggerPepXML method) (alphabase.psm_reader.msfragger_reader.MSFraggerPepXMLReader method) (alphabase.psm_reader.msfragger_reader.MSFraggerPsmTsvReader method) (alphabase.psm_reader.psm_reader.PSMReaderBase method) (alphabase.psm_reader.psm_reader.PSMReaderProvider method) (alphabase.spectral_library.base.SpecLibBase method) (alphabase.spectral_library.decoy.DIANNDecoyGenerator method) (alphabase.spectral_library.decoy.PseudoReverseDecoyGenerator method) (alphabase.spectral_library.decoy.SpecLibDecoy method) (alphabase.spectral_library.decoy.SpecLibDecoyProvider method) (alphabase.spectral_library.flat.SpecLibFlat method) (alphabase.spectral_library.reader.LibraryReaderBase method) (alphabase.spectral_library.translate.WritingProcess method) A A (alphabase.peptide.fragment.Series attribute) AA_ASCII_MASS (in module alphabase.constants.aa) AA_DF (in module alphabase.constants.aa) abundance_convolution() (in module alphabase.constants.isotope) add_charge() (alphabase.protein.fasta.SpecLibFasta method) add_column_mapping() (alphabase.pg_reader.pg_reader.PGReaderBase method) (alphabase.psm_reader.psm_reader.PSMReaderBase method) add_dataset() (alphabase.io.hdf.HDF_Group method) add_group() (alphabase.io.hdf.HDF_Group method) add_modification_mapping() (alphabase.psm_reader.psm_reader.PSMReaderBase method) add_modifications() (alphabase.protein.fasta.SpecLibFasta method) add_modifications_for_lower_case_AA() (in module alphabase.constants.modification) add_mods_for_one_seq() (alphabase.protein.fasta.SpecLibFasta method) add_new_frag_type() (in module alphabase.peptide.fragment) add_new_modifications() (in module alphabase.constants.modification) add_peptide_labeling() (alphabase.protein.fasta.SpecLibFasta method) add_single_peptide_labeling() (in module alphabase.protein.fasta) add_special_modifications() (alphabase.protein.fasta.SpecLibFasta method) ADDH (alphabase.peptide.fragment.Loss attribute) alphabase.constants.aa module alphabase.constants.atom module alphabase.constants.isotope module alphabase.constants.modification module alphabase.io.hdf module alphabase.io.tempmmap module alphabase.peptide.fragment module alphabase.peptide.mass_calc module alphabase.peptide.mobility module alphabase.peptide.precursor module alphabase.pg_reader.alphadia_pg_reader module alphabase.pg_reader.alphapept_pg_reader module alphabase.pg_reader.diann_pg_reader module alphabase.pg_reader.fragpipe_pg_reader module alphabase.pg_reader.maxquant_pg_reader module alphabase.pg_reader.mztab_pg_reader module alphabase.pg_reader.pg_reader module alphabase.pg_reader.spectronaut_reader module alphabase.protein.fasta module alphabase.protein.protein_level_decoy module alphabase.psm_reader.alphapept_reader module alphabase.psm_reader.dia_psm_reader module alphabase.psm_reader.maxquant_reader module alphabase.psm_reader.msfragger_reader module alphabase.psm_reader.pfind_reader module alphabase.psm_reader.psm_reader module alphabase.spectral_library.base module alphabase.spectral_library.decoy module alphabase.spectral_library.flat module alphabase.spectral_library.reader module alphabase.spectral_library.translate module AlphaDiaPGReader (class in alphabase.pg_reader.alphadia_pg_reader) AlphaPeptPGReader (class in alphabase.pg_reader.alphapept_pg_reader) AlphaPeptReader (class in alphabase.psm_reader.alphapept_reader) annotate_fragments_from_speclib() (alphabase.spectral_library.base.SpecLibBase method) (in module alphabase.spectral_library.base) annotate_precursor_df() (in module alphabase.protein.fasta) ANY_C_TERM (alphabase.constants.modification.ModificationKeys attribute) ANY_C_TERM_SPECIFIC (alphabase.constants.modification.ModificationKeys attribute) ANY_N_TERM (alphabase.constants.modification.ModificationKeys attribute) ANY_N_TERM_SPECIFIC (alphabase.constants.modification.ModificationKeys attribute) append() (alphabase.io.hdf.HDF_Dataframe method) (alphabase.io.hdf.HDF_Dataset method) (alphabase.spectral_library.base.SpecLibBase method) append_decoy_sequence() (alphabase.spectral_library.base.SpecLibBase method) append_protein_name() (alphabase.protein.fasta.SpecLibFasta method) append_special_modifications() (in module alphabase.protein.fasta) append_to_target_lib() (alphabase.protein.protein_level_decoy.ProteinReverseDecoy method) (alphabase.spectral_library.decoy.SpecLibDecoy method) array() (in module alphabase.io.tempmmap) available_dense_fragment_dfs() (alphabase.spectral_library.base.SpecLibBase method) B B (alphabase.peptide.fragment.Series attribute) BaseDecoyGenerator (class in alphabase.spectral_library.decoy) C C (alphabase.peptide.fragment.Series attribute) calc_AA_masses() (in module alphabase.constants.aa) calc_AA_masses_for_same_len_seqs() (in module alphabase.constants.aa) calc_AA_masses_for_var_len_seqs() (in module alphabase.constants.aa) calc_and_clip_precursor_mz() (alphabase.spectral_library.base.SpecLibBase method) calc_b_y_and_peptide_mass() (in module alphabase.peptide.mass_calc) calc_b_y_and_peptide_masses_for_same_len_seqs() (in module alphabase.peptide.mass_calc) calc_dense_fragments() (alphabase.spectral_library.flat.SpecLibFlat method) calc_diff_modification_mass() (in module alphabase.peptide.mass_calc) calc_formula_distribution() (alphabase.constants.isotope.IsotopeDistribution method) calc_fragment_cardinality() (in module alphabase.peptide.fragment) calc_fragment_count() (alphabase.spectral_library.base.SpecLibBase method) (in module alphabase.peptide.fragment) calc_fragment_mz_df() (alphabase.spectral_library.base.SpecLibBase method) calc_fragment_mz_values_for_same_nAA() (in module alphabase.peptide.fragment) calc_mass_from_formula() (in module alphabase.constants.atom) calc_mod_diff_masses_for_same_len_seqs() (in module alphabase.peptide.mass_calc) calc_mod_masses_for_same_len_seqs() (in module alphabase.constants.modification) calc_modification_mass() (in module alphabase.constants.modification) calc_modification_mass_sum() (in module alphabase.constants.modification) calc_modloss_mass() (in module alphabase.constants.modification) calc_modloss_mass_with_importance() (in module alphabase.constants.modification) calc_peptide_masses_for_same_len_seqs() (in module alphabase.peptide.mass_calc) calc_precursor_isotope() (alphabase.spectral_library.base.SpecLibBase method) (in module alphabase.peptide.precursor) calc_precursor_isotope_info() (alphabase.spectral_library.base.SpecLibBase method) (in module alphabase.peptide.precursor) calc_precursor_isotope_info_mp() (in module alphabase.peptide.precursor) calc_precursor_isotope_intensity() (alphabase.spectral_library.base.SpecLibBase method) (in module alphabase.peptide.precursor) calc_precursor_isotope_intensity_mp() (in module alphabase.peptide.precursor) calc_precursor_isotope_mp() (in module alphabase.peptide.precursor) calc_precursor_mz() (alphabase.spectral_library.base.SpecLibBase method) (in module alphabase.peptide.precursor) calc_sequence_masses_for_same_len_seqs() (in module alphabase.constants.aa) ccs_to_mobility_bruker() (in module alphabase.peptide.mobility) ccs_to_mobility_for_df() (in module alphabase.peptide.mobility) charged_frag_types (alphabase.spectral_library.base.SpecLibBase attribute) CHEM_INFO_DICT (in module alphabase.constants.atom) CHEM_ISOTOPE_DIST (in module alphabase.constants.atom) CHEM_MONO_IDX (in module alphabase.constants.atom) CHEM_MONO_MASS (in module alphabase.constants.atom) ChemicalCompositonFormula (class in alphabase.constants.atom) clear() (in module alphabase.io.tempmmap) cleave_sequence() (alphabase.protein.fasta.Digest method) cleave_sequence_with_cut_pos() (in module alphabase.protein.fasta) clip_by_precursor_mz_() (alphabase.spectral_library.base.SpecLibBase method) column_mapping (alphabase.pg_reader.fragpipe_pg_reader.FragPipePGReader attribute) (alphabase.pg_reader.mztab_pg_reader.MZTabPGReader attribute) (alphabase.pg_reader.pg_reader.PGReaderBase attribute) (alphabase.psm_reader.psm_reader.PSMReaderBase attribute) columns (alphabase.io.hdf.HDF_Dataframe property) components (alphabase.io.hdf.HDF_Group property) compress_fragment_indices() (in module alphabase.peptide.fragment) concat_precursor_fragment_dataframes() (in module alphabase.peptide.fragment) concat_proteins() (in module alphabase.protein.fasta) copy() (alphabase.spectral_library.base.SpecLibBase method) create_dense_matrices() (in module alphabase.peptide.fragment) create_empty_mmap() (in module alphabase.io.tempmmap) create_fragment_mz_dataframe() (in module alphabase.peptide.fragment) create_fragment_mz_dataframe_by_sort_precursor() (in module alphabase.peptide.fragment) create_labeling_peptide_df() (in module alphabase.protein.fasta) create_mmap() (alphabase.io.hdf.HDF_Dataset method) create_modified_sequence() (in module alphabase.spectral_library.translate) custom_fragment_df_columns (alphabase.spectral_library.flat.SpecLibFlat attribute) D dataframe_names (alphabase.io.hdf.HDF_Group property) dataframes (alphabase.io.hdf.HDF_Group property) dataset_names (alphabase.io.hdf.HDF_Group property) datasets (alphabase.io.hdf.HDF_Group property) decoy (alphabase.spectral_library.base.SpecLibBase attribute) decoy_lib_provider (in module alphabase.spectral_library.decoy) decoy_sequence() (alphabase.protein.protein_level_decoy.ProteinReverseDecoy method) (alphabase.spectral_library.decoy.SpecLibDecoy method) delete_mmap() (alphabase.io.hdf.HDF_Dataset method) delta_formula (alphabase.peptide.fragment.FragmentType attribute) delta_mass (alphabase.peptide.fragment.FragmentType attribute), [1] DIANNDecoyGenerator (class in alphabase.spectral_library.decoy) DiannPGReader (class in alphabase.pg_reader.diann_pg_reader) DiannReader (class in alphabase.psm_reader.dia_psm_reader) Digest (class in alphabase.protein.fasta) Direction (class in alphabase.peptide.fragment) direction_id (alphabase.peptide.fragment.FragmentType attribute) dtype (alphabase.io.hdf.HDF_Dataframe property) (alphabase.io.hdf.HDF_Dataset property) E editing_mode() (alphabase.io.hdf.HDF_Object method) element_to_cum_dist_dict (alphabase.constants.isotope.IsotopeDistribution attribute) element_to_cum_mono_idx (alphabase.constants.isotope.IsotopeDistribution attribute) F file_name (alphabase.io.hdf.HDF_Object property) fill_in_indices() (in module alphabase.peptide.fragment) filter_fragment_number() (alphabase.spectral_library.base.SpecLibBase method) (in module alphabase.peptide.fragment) filter_psm_by_modifications() (alphabase.psm_reader.psm_reader.PSMReaderBase method) filter_valid_charged_frag_types() (in module alphabase.peptide.fragment) flatten_fragments() (in module alphabase.peptide.fragment) formula_dist() (in module alphabase.constants.isotope) FORWARD (alphabase.peptide.fragment.Direction attribute) fragment_df (alphabase.spectral_library.flat.SpecLibFlat property) fragment_intensity_df (alphabase.spectral_library.base.SpecLibBase property) fragment_mz_df (alphabase.spectral_library.base.SpecLibBase property) FragmentType (class in alphabase.peptide.fragment) FragPipePGReader (class in alphabase.pg_reader.fragpipe_pg_reader) from_smiles() (alphabase.constants.atom.ChemicalCompositonFormula class method) G get_available_columns() (in module alphabase.spectral_library.base) get_candidate_sites() (in module alphabase.protein.fasta) get_charged_frag_types() (in module alphabase.peptide.fragment) get_cut_positions() (alphabase.protein.fasta.Digest method) get_decoy_lib() (alphabase.spectral_library.decoy.SpecLibDecoyProvider method) get_fix_mods() (in module alphabase.protein.fasta) get_full_charged_types() (alphabase.spectral_library.flat.SpecLibFlat method) get_mod_seq_charge_hash() (in module alphabase.peptide.precursor) get_mod_seq_formula() (in module alphabase.peptide.precursor) get_mod_seq_hash() (in module alphabase.peptide.precursor) get_mod_seq_isotope_distribution() (in module alphabase.peptide.precursor) get_peptides_from_fasta() (alphabase.protein.fasta.SpecLibFasta method) get_peptides_from_fasta_list() (alphabase.protein.fasta.SpecLibFasta method) get_peptides_from_peptide_sequence_list() (alphabase.protein.fasta.SpecLibFasta method) get_peptides_from_protein_df() (alphabase.protein.fasta.SpecLibFasta method) get_peptides_from_protein_dict() (alphabase.protein.fasta.SpecLibFasta method) get_pFind_mods() (in module alphabase.psm_reader.pfind_reader) get_preconfigured_regex() (alphabase.pg_reader.pg_reader.PGReaderBase class method) get_reader() (alphabase.pg_reader.pg_reader.PGReaderProvider method) (alphabase.psm_reader.psm_reader.PSMReaderProvider method) get_reader_by_yaml() (alphabase.pg_reader.pg_reader.PGReaderProvider method) (alphabase.psm_reader.psm_reader.PSMReaderProvider method) get_reduced_mass() (in module alphabase.peptide.mobility) get_right_most_isotope_offset() (in module alphabase.peptide.precursor) get_sliced_fragment_dataframe() (in module alphabase.peptide.fragment) get_uniprot_gene_name() (in module alphabase.protein.fasta) get_var_mod_sites() (in module alphabase.protein.fasta) get_var_mods() (in module alphabase.protein.fasta) get_var_mods_per_sites() (in module alphabase.protein.fasta) get_var_mods_per_sites_multi_mods_on_aa() (in module alphabase.protein.fasta) get_var_mods_per_sites_single_mod_on_aa() (in module alphabase.protein.fasta) group_names (alphabase.io.hdf.HDF_Group property) groups (alphabase.io.hdf.HDF_Group property) H H2O (alphabase.peptide.fragment.Loss attribute) has_custom_mods() (in module alphabase.constants.modification) hash_mod_seq_charge_df() (in module alphabase.peptide.precursor) hash_mod_seq_df() (in module alphabase.peptide.precursor) hash_precursor_df() (alphabase.spectral_library.base.SpecLibBase method) (in module alphabase.peptide.precursor) HDF_Dataframe (class in alphabase.io.hdf) HDF_Dataset (class in alphabase.io.hdf) HDF_File (class in alphabase.io.hdf) HDF_Group (class in alphabase.io.hdf) HDF_Object (class in alphabase.io.hdf) I import_and_process_fasta() (alphabase.protein.fasta.SpecLibFasta method) import_and_process_peptide_sequences() (alphabase.protein.fasta.SpecLibFasta method) import_and_process_protein_df() (alphabase.protein.fasta.SpecLibFasta method) import_and_process_protein_dict() (alphabase.protein.fasta.SpecLibFasta method) import_file() (alphabase.pg_reader.pg_reader.PGReaderBase method) (alphabase.psm_reader.psm_reader.PSMReaderBase method) import_files() (alphabase.psm_reader.psm_reader.PSMReaderBase method) init_fragment_by_precursor_dataframe() (in module alphabase.peptide.fragment) init_fragment_dataframe_from_other() (in module alphabase.peptide.fragment) init_zero_fragment_dataframe() (in module alphabase.peptide.fragment) is_nterm_frag() (in module alphabase.spectral_library.translate) is_precursor_refined() (in module alphabase.peptide.precursor) is_precursor_sorted() (in module alphabase.peptide.precursor) IsotopeDistribution (class in alphabase.constants.isotope) J join_left() (in module alphabase.peptide.fragment) K keep_modloss_by_importance() (in module alphabase.constants.modification) keep_top_k_fragments (alphabase.spectral_library.flat.SpecLibFlat attribute) key_numeric_columns (alphabase.spectral_library.base.SpecLibBase attribute) (alphabase.spectral_library.flat.SpecLibFlat attribute) L LibraryReaderBase (class in alphabase.spectral_library.reader) load() (alphabase.psm_reader.psm_reader.PSMReaderBase method) load_all_proteins() (in module alphabase.protein.fasta) load_df_from_hdf() (alphabase.spectral_library.base.SpecLibBase method) load_elem_yaml() (in module alphabase.constants.atom) load_fasta_list_as_protein_df() (in module alphabase.protein.fasta) load_hdf() (alphabase.protein.fasta.SpecLibFasta method) (alphabase.spectral_library.base.SpecLibBase method) (alphabase.spectral_library.flat.SpecLibFlat method) load_mod_df() (in module alphabase.constants.modification) Loss (class in alphabase.peptide.fragment) loss_id (alphabase.peptide.fragment.FragmentType attribute) LOSSH (alphabase.peptide.fragment.Loss attribute) M mask_fragment_intensity_by_frag_nAA() (in module alphabase.spectral_library.translate) mask_fragment_intensity_by_mz_() (in module alphabase.spectral_library.translate) mask_fragments_for_charge_greater_than_precursor_charge() (in module alphabase.peptide.fragment) max_peptidoform_num (alphabase.protein.fasta.SpecLibFasta attribute) max_precursor_mz (alphabase.spectral_library.base.SpecLibBase attribute) MaxQuantPGReader (class in alphabase.pg_reader.maxquant_pg_reader) MaxQuantReader (class in alphabase.psm_reader.maxquant_reader) measurement_regex (alphabase.pg_reader.fragpipe_pg_reader.FragPipePGReader attribute) (alphabase.pg_reader.mztab_pg_reader.MZTabPGReader attribute) (alphabase.pg_reader.pg_reader.PGReaderBase attribute) merge_precursor_fragment_df() (in module alphabase.spectral_library.translate) metadata (alphabase.io.hdf.HDF_Object property) min_fragment_intensity (alphabase.spectral_library.flat.SpecLibFlat attribute) min_precursor_mz (alphabase.spectral_library.base.SpecLibBase attribute) mmap (alphabase.io.hdf.HDF_Dataset property) mmap_array_from_path() (in module alphabase.io.tempmmap) mobility_to_ccs_bruker() (in module alphabase.peptide.mobility) mobility_to_ccs_for_df() (in module alphabase.peptide.mobility) MOD_CHEM (in module alphabase.constants.modification) MOD_DF (in module alphabase.constants.modification) MOD_LOSS_IMPORTANCE (in module alphabase.constants.modification) MOD_LOSS_MASS (in module alphabase.constants.modification) MOD_MASS (in module alphabase.constants.modification) modification_mapping (alphabase.psm_reader.psm_reader.PSMReaderBase attribute) (alphabase.psm_reader.psm_reader.PSMReaderBase property) ModificationKeys (class in alphabase.constants.modification) ModifiedSequenceReader (class in alphabase.psm_reader.maxquant_reader) modloss (alphabase.peptide.fragment.FragmentType attribute) MODLOSS (alphabase.peptide.fragment.Loss attribute) module alphabase.constants.aa alphabase.constants.atom alphabase.constants.isotope alphabase.constants.modification alphabase.io.hdf alphabase.io.tempmmap alphabase.peptide.fragment alphabase.peptide.mass_calc alphabase.peptide.mobility alphabase.peptide.precursor alphabase.pg_reader.alphadia_pg_reader alphabase.pg_reader.alphapept_pg_reader alphabase.pg_reader.diann_pg_reader alphabase.pg_reader.fragpipe_pg_reader alphabase.pg_reader.maxquant_pg_reader alphabase.pg_reader.mztab_pg_reader alphabase.pg_reader.pg_reader alphabase.pg_reader.spectronaut_reader alphabase.protein.fasta alphabase.protein.protein_level_decoy alphabase.psm_reader.alphapept_reader alphabase.psm_reader.dia_psm_reader alphabase.psm_reader.maxquant_reader alphabase.psm_reader.msfragger_reader alphabase.psm_reader.pfind_reader alphabase.psm_reader.psm_reader alphabase.spectral_library.base alphabase.spectral_library.decoy alphabase.spectral_library.flat alphabase.spectral_library.reader alphabase.spectral_library.translate MSFraggerModificationTranslator (class in alphabase.psm_reader.msfragger_reader) MSFraggerPepXML (class in alphabase.psm_reader.msfragger_reader) MSFraggerPepXMLReader (class in alphabase.psm_reader.msfragger_reader) MSFraggerPsmTsvReader (class in alphabase.psm_reader.msfragger_reader) MZTabPGReader (class in alphabase.pg_reader.mztab_pg_reader) N name (alphabase.io.hdf.HDF_Object property) (alphabase.peptide.fragment.FragmentType attribute) NH3 (alphabase.peptide.fragment.Loss attribute) NONE (alphabase.peptide.fragment.Loss attribute) normalize_rt_by_raw_name() (alphabase.psm_reader.psm_reader.PSMReaderBase method) O one_element_dist() (in module alphabase.constants.isotope) ones() (in module alphabase.io.tempmmap) P parse_all_frag_type_representation() (in module alphabase.peptide.fragment) parse_ap() (in module alphabase.psm_reader.alphapept_reader) parse_base_library() (alphabase.spectral_library.flat.SpecLibFlat method) parse_charged_frag_type() (in module alphabase.peptide.fragment) parse_formula() (in module alphabase.constants.atom) parse_fragment() (in module alphabase.peptide.fragment) parse_labels() (in module alphabase.protein.fasta) parse_mod_seq() (in module alphabase.psm_reader.maxquant_reader) parse_pfind_protein() (in module alphabase.psm_reader.pfind_reader) parse_term_mod() (in module alphabase.protein.fasta) peptide_df (alphabase.spectral_library.base.SpecLibBase property) pFindReader (class in alphabase.psm_reader.pfind_reader) pg_reader_provider (in module alphabase.pg_reader.pg_reader) PGReaderBase (class in alphabase.pg_reader.pg_reader) PGReaderProvider (class in alphabase.pg_reader.pg_reader) precursor_df (alphabase.spectral_library.base.SpecLibBase property) process_from_naked_peptide_seqs() (alphabase.protein.fasta.SpecLibFasta method) protease_dict (in module alphabase.protein.fasta) PROTEIN_C_TERM (alphabase.constants.modification.ModificationKeys attribute) PROTEIN_C_TERM_SPECIFIC (alphabase.constants.modification.ModificationKeys attribute) protein_df (alphabase.protein.fasta.SpecLibFasta attribute) (alphabase.spectral_library.flat.SpecLibFlat property) protein_idxes_to_names() (in module alphabase.protein.fasta) PROTEIN_N_TERM (alphabase.constants.modification.ModificationKeys attribute) PROTEIN_N_TERM_SPECIFIC (alphabase.constants.modification.ModificationKeys attribute) ProteinReverseDecoy (class in alphabase.protein.protein_level_decoy) PseudoReverseDecoyGenerator (class in alphabase.spectral_library.decoy) psm_df (alphabase.psm_reader.psm_reader.PSMReaderBase attribute) (alphabase.psm_reader.psm_reader.PSMReaderBase property) psm_reader_provider (in module alphabase.psm_reader.psm_reader) psm_reader_yaml (in module alphabase.psm_reader.psm_reader) PSMReaderBase (class in alphabase.psm_reader.psm_reader) PSMReaderProvider (class in alphabase.psm_reader.psm_reader) R read_fasta_file() (in module alphabase.protein.fasta) read_only (alphabase.io.hdf.HDF_Object property) redefine_temp_location() (in module alphabase.io.tempmmap) ref_ion (alphabase.peptide.fragment.FragmentType attribute) refine_df() (alphabase.spectral_library.base.SpecLibBase method) refine_precursor_df() (in module alphabase.peptide.precursor) register() (alphabase.spectral_library.decoy.SpecLibDecoyProvider method) register_reader() (alphabase.pg_reader.pg_reader.PGReaderProvider method) (alphabase.psm_reader.psm_reader.PSMReaderProvider method) register_readers() (in module alphabase.psm_reader.alphapept_reader) (in module alphabase.psm_reader.dia_psm_reader) (in module alphabase.psm_reader.maxquant_reader) (in module alphabase.psm_reader.msfragger_reader) (in module alphabase.psm_reader.pfind_reader) remove_unused_fragments() (alphabase.spectral_library.base.SpecLibBase method) (alphabase.spectral_library.flat.SpecLibFlat method) (in module alphabase.peptide.fragment) replace_atoms() (in module alphabase.constants.aa) replace_parentheses_with_brackets() (in module alphabase.psm_reader.maxquant_reader) reset_AA_atoms() (in module alphabase.constants.aa) reset_AA_Composition() (in module alphabase.constants.aa) reset_AA_df() (in module alphabase.constants.aa) reset_AA_mass() (in module alphabase.constants.aa) reset_elements() (in module alphabase.constants.atom) reset_precursor_df() (in module alphabase.peptide.precursor) REVERSE (alphabase.peptide.fragment.Direction attribute) run() (alphabase.spectral_library.translate.WritingProcess method) S save_df_to_hdf() (alphabase.spectral_library.base.SpecLibBase method) save_hdf() (alphabase.protein.fasta.SpecLibFasta method) (alphabase.spectral_library.base.SpecLibBase method) (alphabase.spectral_library.flat.SpecLibFlat method) SEPARATOR (alphabase.constants.modification.ModificationKeys attribute) Series (class in alphabase.peptide.fragment) series_id (alphabase.peptide.fragment.FragmentType attribute) set_modification_mapping() (alphabase.psm_reader.psm_reader.PSMReaderBase method) set_read_only() (alphabase.io.hdf.HDF_Group method) (alphabase.io.hdf.HDF_Object method) set_slice() (alphabase.io.hdf.HDF_Dataframe method) (alphabase.io.hdf.HDF_Dataset method) set_truncate() (alphabase.io.hdf.HDF_Group method) (alphabase.io.hdf.HDF_Object method) shape (alphabase.io.hdf.HDF_Dataset property) SITE_SEPARATOR (alphabase.constants.modification.ModificationKeys attribute) sort_charged_frag_types() (in module alphabase.peptide.fragment) speclib_to_single_df() (in module alphabase.spectral_library.translate) speclib_to_swath_df() (in module alphabase.spectral_library.translate) SpecLibBase (class in alphabase.spectral_library.base) SpecLibDecoy (class in alphabase.spectral_library.decoy) SpecLibDecoyProvider (class in alphabase.spectral_library.decoy) SpecLibFasta (class in alphabase.protein.fasta) SpecLibFlat (class in alphabase.spectral_library.flat) SpectronautPGReader (class in alphabase.pg_reader.spectronaut_reader) SpectronautReader (class in alphabase.psm_reader.dia_psm_reader) SpectronautReportReader (class in alphabase.psm_reader.dia_psm_reader) SWATHLibraryReader (in module alphabase.spectral_library.reader) SwathReader (class in alphabase.psm_reader.dia_psm_reader) T target_lib (alphabase.protein.protein_level_decoy.ProteinReverseDecoy attribute) (alphabase.spectral_library.decoy.SpecLibDecoy attribute) TERM_SEPARATOR (alphabase.constants.modification.ModificationKeys attribute) to_speclib_base() (alphabase.spectral_library.flat.SpecLibFlat method) to_SpecLibBase() (alphabase.spectral_library.flat.SpecLibFlat method) translate() (alphabase.psm_reader.msfragger_reader.MSFraggerModificationTranslator method) translate_pFind_mod() (in module alphabase.psm_reader.pfind_reader) translate_to_decoy() (alphabase.spectral_library.decoy.SpecLibDecoy method) translate_to_tsv() (in module alphabase.spectral_library.translate) truncate (alphabase.io.hdf.HDF_Object property) truncate_isotope() (in module alphabase.constants.atom) U update_all_by_MOD_DF() (in module alphabase.constants.modification) update_an_AA() (in module alphabase.constants.aa) update_atom_infos() (in module alphabase.constants.atom) update_precursor_mz() (in module alphabase.peptide.precursor) update_sliced_fragment_dataframe() (in module alphabase.peptide.fragment) V values (alphabase.io.hdf.HDF_Dataframe property) (alphabase.io.hdf.HDF_Dataset property) W WritingProcess (class in alphabase.spectral_library.translate) X X (alphabase.peptide.fragment.Series attribute) Y Y (alphabase.peptide.fragment.Series attribute) Z Z (alphabase.peptide.fragment.Series attribute) zeros() (in module alphabase.io.tempmmap)