Index

A

add_columns() (in module mutcleaner.cleaners.basic_cleaners) add_delayed_step() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) add_mutation() (mutcleaner.core.mutation.MutationSet method) add_mutation_set() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) add_mutation_sets() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) add_reference_sequence() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) add_reference_sequences_by_target() (in module mutcleaner.cleaners.rbd_custom_cleaner) add_sequences_to_dataset() (in module mutcleaner.cleaners.basic_cleaners) add_wild_type_sequences_by_library() (in module mutcleaner.cleaners.archstabms_1e10_custom_cleaners) aggregate_labels_by_name() (in module mutcleaner.cleaners.basic_cleaners) aggregation_strategy (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.MGnifyddGCleanerConfig attribute) ambler_to_seq_mapping (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute)

AminoAcidMutation (class in mutcleaner.core.mutation) AminoAcidMutationSet (class in mutcleaner.core) (class in mutcleaner.core.mutation) AntitoxinParD3CleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.antitoxin_pard3_cleaner) apply() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) apply_mutation() (mutcleaner.core.sequence.BaseSequence method) apply_mutations_to_sequences() (in module mutcleaner.cleaners.basic_cleaners) apply_single_mutation() (in module mutcleaner.utils.cleaner_workers) ArchStabMS1E10CleanerSup4Config (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.archstabms_1e10_sup4_cleaner) ArchStabMS1E10CleanerSup5Config (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.archstabms_1e10_sup5_cleaner) artifacts (mutcleaner.core.Pipeline property) (mutcleaner.core.pipeline.Pipeline property) assign() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) average_labels_by_name() (in module mutcleaner.cleaners.basic_cleaners)

B

back_transcribe() (mutcleaner.core.RNASequence method) (mutcleaner.core.sequence.RNASequence method) BaseAlphabet (class in mutcleaner.core.alphabet)

BaseCleanerConfig (class in mutcleaner.cleaners.base_config) BaseMutation (class in mutcleaner.core.mutation) BaseSequence (class in mutcleaner.core.sequence)

C

CDNAProteolysisCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.cdna_proteolysis_cleaner) ChitosanasedTmCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.chitosanase_dtm_cleaner) clean_antitoxin_pard3_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.antitoxin_pard3_cleaner) clean_archstabms_1e10_sup4_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.archstabms_1e10_sup4_cleaner) clean_archstabms_1e10_sup5_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.archstabms_1e10_sup5_cleaner) clean_cdna_proteolysis_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.cdna_proteolysis_cleaner) clean_chitosanase_dtm_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.chitosanase_dtm_cleaner) clean_codon_cdna_proteolysis_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.codon_cdna_proteolysis_cleaner) clean_ctxm_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.ctxm_cleaner) clean_ddg_dtm_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.ddg_dtm_cleaners) clean_human_domainome_sup2_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.human_domainome_sup2_cleaner) clean_human_domainome_sup4_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.human_domainome_sup4_cleaner) clean_human_myoglobin_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.human_myoglobin_cleaner) clean_mgnify_ddg_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.mgnify_ddg_cleaner) clean_proteingym_dms_substitutions_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.proteingym_dms_substitutions_cleaner) clean_rbd_ace2_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.rbd_ace2_cleaner) clean_rbd_antibody_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.rbd_antibody_cleaner) clean_trpb_dataset() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.trpb_cleaner) CodoncDNAProteolysisCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.codon_cdna_proteolysis_cleaner) CodonMutation (class in mutcleaner.core.mutation) CodonMutationSet (class in mutcleaner.core) (class in mutcleaner.core.mutation) CodonTable (class in mutcleaner.core) (class in mutcleaner.core.codon) column_mapping (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup4_cleaner.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup5_cleaner.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.chitosanase_dtm_cleaner.ChitosanasedTmCleanerConfig attribute) (mutcleaner.cleaners.ChitosanasedTmCleanerConfig attribute) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig attribute) (mutcleaner.cleaners.TrpBCleanerConfig attribute)

columns_to_add (mutcleaner.cleaners.chitosanase_dtm_cleaner.ChitosanasedTmCleanerConfig attribute) (mutcleaner.cleaners.ChitosanasedTmCleanerConfig attribute) compute_mutations() (in module mutcleaner.cleaners.archstabms_1e10_custom_cleaners) convert_codon_to_amino_acid() (in module mutcleaner.cleaners.human_myoglobin_custom_cleaners) convert_codon_to_amino_acid_sets() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) convert_data_types() (in module mutcleaner.cleaners.basic_cleaners) (in module mutcleaner.utils.type_converter) convert_data_types_batch() (in module mutcleaner.utils.type_converter) convert_format_1() (in module mutcleaner.utils.dataset_builders) convert_format_2() (in module mutcleaner.utils.dataset_builders) convert_pairwise_couplings_to_ddg() (in module mutcleaner.cleaners.archstabms_1e10_custom_cleaners) convert_to_boolean() (in module mutcleaner.utils.type_converter) convert_to_mutation_dataset_format() (in module mutcleaner.cleaners.basic_cleaners) copy() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) count_by_effect_type() (mutcleaner.core.AminoAcidMutationSet method) (mutcleaner.core.mutation.AminoAcidMutationSet method) create_antitoxin_pard3_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.antitoxin_pard3_cleaner) create_archstabms_1e10_sup4_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.archstabms_1e10_sup4_cleaner) create_archstabms_1e10_sup5_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.archstabms_1e10_sup5_cleaner) create_cdna_proteolysis_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.cdna_proteolysis_cleaner) create_chitosanase_dtm_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.chitosanase_dtm_cleaner) create_codon_cdna_proteolysis_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.codon_cdna_proteolysis_cleaner) create_ctxm_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.ctxm_cleaner) create_ddg_dtm_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.ddg_dtm_cleaners) create_human_domainome_sup2_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.human_domainome_sup2_cleaner) create_human_domainome_sup4_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.human_domainome_sup4_cleaner) create_human_myoglobin_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.human_myoglobin_cleaner) create_mgnify_ddg_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.mgnify_ddg_cleaner) create_pipeline() (in module mutcleaner.core) (in module mutcleaner.core.pipeline) create_proteingym_dms_substitutions_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.proteingym_dms_substitutions_cleaner) create_rbd_ace2_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.rbd_ace2_cleaner) create_rbd_antibody_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.rbd_antibody_cleaner) create_trpb_cleaner() (in module mutcleaner.cleaners) (in module mutcleaner.cleaners.trpb_cleaner) CTXMCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.ctxm_cleaner)

D

data (mutcleaner.core.Pipeline property) (mutcleaner.core.pipeline.Pipeline property) DdgDtmCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.ddg_dtm_cleaners) default_alphabet() (mutcleaner.core.DNASequence class method) (mutcleaner.core.ProteinSequence class method) (mutcleaner.core.RNASequence class method) (mutcleaner.core.sequence.BaseSequence class method) (mutcleaner.core.sequence.DNASequence class method) (mutcleaner.core.sequence.ProteinSequence class method) (mutcleaner.core.sequence.RNASequence class method) delayed_then() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) DNAAlphabet (class in mutcleaner.core) (class in mutcleaner.core.alphabet) DNASequence (class in mutcleaner.core) (class in mutcleaner.core.sequence) download() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_antitoxin_pard3_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_archstabms1e10_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_chitosanase_dtm_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_ctxm_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader)

download_ddg_dtm_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_human_domainome_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_human_myoglobin_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_mgnify_ddg_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_protein_cdna_proteolysis_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_proteingym_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_rbd_ace2_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_rbd_antibody_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) download_trpb_source_file() (in module mutcleaner.utils) (in module mutcleaner.utils.raw_data_downloader) drop_na_columns (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute)

E

effect_type (mutcleaner.core.mutation.AminoAcidMutation property) execute() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method)

expand_mutations() (in module mutcleaner.cleaners.ctxm_custom_cleaner) extract_and_rename_columns() (in module mutcleaner.cleaners.basic_cleaners) extract_domain_sequences() (in module mutcleaner.cleaners.human_domainome_custom_cleaners)

F

fallback_reference_sequence (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) filter() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) filter_and_clean_data() (in module mutcleaner.cleaners.basic_cleaners) filter_by_category() (mutcleaner.core.mutation.MutationSet method) filter_by_effect_type() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) filter_by_mutation_type() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) filter_by_reference() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) filters (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup4_cleaner.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup5_cleaner.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig attribute) (mutcleaner.cleaners.TrpBCleanerConfig attribute)

find_motif() (mutcleaner.core.ProteinSequence method) (mutcleaner.core.sequence.ProteinSequence method) from_dataframe() (mutcleaner.core.dataset.MutationDataset class method) (mutcleaner.core.MutationDataset class method) from_dict() (mutcleaner.cleaners.base_config.BaseCleanerConfig class method) from_json() (mutcleaner.cleaners.base_config.BaseCleanerConfig class method) from_string() (mutcleaner.core.mutation.AminoAcidMutation class method) (mutcleaner.core.mutation.BaseMutation class method) (mutcleaner.core.mutation.CodonMutation class method) (mutcleaner.core.mutation.MutationSet class method)

G

generate_mutation_strings() (in module mutcleaner.cleaners.human_domainome_custom_cleaners) get_all_artifacts() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) get_artifact() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) get_conversion_function() (in module mutcleaner.utils.type_converter) get_data() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) get_delayed_steps_info() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) get_execution_summary() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) get_invalid_chars() (mutcleaner.core.alphabet.BaseAlphabet method) get_missense_mutations() (mutcleaner.core.AminoAcidMutationSet method) (mutcleaner.core.mutation.AminoAcidMutationSet method) get_mutation_at() (mutcleaner.core.mutation.MutationSet method) get_mutation_categories() (mutcleaner.core.mutation.MutationSet method) get_mutation_category() (mutcleaner.core.mutation.AminoAcidMutation method) (mutcleaner.core.mutation.BaseMutation method) (mutcleaner.core.mutation.CodonMutation method) get_mutation_count() (mutcleaner.core.mutation.MutationSet method) get_mutation_set_label() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) get_mutation_set_reference() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) get_nonsense_mutations() (mutcleaner.core.AminoAcidMutationSet method) (mutcleaner.core.mutation.AminoAcidMutationSet method)

get_one_letter_code() (mutcleaner.core.alphabet.ProteinAlphabet method) (mutcleaner.core.ProteinAlphabet method) get_position_coverage() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) get_positions() (mutcleaner.core.mutation.MutationSet method) get_positions_set() (mutcleaner.core.mutation.MutationSet method) get_reference_sequence() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) get_residue() (mutcleaner.core.ProteinSequence method) (mutcleaner.core.sequence.ProteinSequence method) get_sorted_by_position() (mutcleaner.core.mutation.MutationSet method) get_standard_table() (mutcleaner.core.codon.CodonTable class method) (mutcleaner.core.CodonTable class method) get_statistics() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) get_step_result() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) get_subsequence() (mutcleaner.core.sequence.BaseSequence method) get_summary() (mutcleaner.cleaners.base_config.BaseCleanerConfig method) get_synonymous_mutations() (mutcleaner.core.AminoAcidMutationSet method) (mutcleaner.core.mutation.AminoAcidMutationSet method) get_table_by_name() (mutcleaner.core.codon.CodonTable class method) (mutcleaner.core.CodonTable class method) get_three_letter_code() (mutcleaner.core.alphabet.ProteinAlphabet method) (mutcleaner.core.ProteinAlphabet method)

H

handle_multiple_wt (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute) has_mutation_at() (mutcleaner.core.mutation.MutationSet method) has_pending_steps (mutcleaner.core.Pipeline property) (mutcleaner.core.pipeline.Pipeline property) has_stop_codon_mutations() (mutcleaner.core.AminoAcidMutationSet method) (mutcleaner.core.mutation.AminoAcidMutationSet method)

header_parser() (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig method) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig method) HumanDomainomeSup2CleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.human_domainome_sup2_cleaner) HumanDomainomeSup4CleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.human_domainome_sup4_cleaner) HumanMyoglobinCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.human_myoglobin_cleaner)

I

infer_mut_workers (mutcleaner.cleaners.chitosanase_dtm_cleaner.ChitosanasedTmCleanerConfig attribute) (mutcleaner.cleaners.ChitosanasedTmCleanerConfig attribute) (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.MGnifyddGCleanerConfig attribute) infer_mutation() (mutcleaner.core.sequence.BaseSequence method) infer_mutations_from_sequences() (in module mutcleaner.cleaners.basic_cleaners) infer_single_mutationset() (in module mutcleaner.utils.cleaner_workers) infer_wildtype_sequences() (in module mutcleaner.cleaners.basic_cleaners) infer_wt_sequence() (in module mutcleaner.cleaners.antitoxin_pard3_custom_cleaners) infer_wt_sequence_grouped() (in module mutcleaner.utils.cleaner_workers) infer_wt_workers (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute)

invert_mutation() (in module mutcleaner.utils.mutation_converter) invert_mutation_set() (in module mutcleaner.utils.mutation_converter) is_missense() (mutcleaner.core.mutation.AminoAcidMutation method) is_multiple_mutations() (mutcleaner.core.mutation.MutationSet method) is_nonsense() (mutcleaner.core.mutation.AminoAcidMutation method) is_single_mutation() (mutcleaner.core.mutation.MutationSet method) is_start_codon() (mutcleaner.core.codon.CodonTable method) (mutcleaner.core.CodonTable method) is_stop_codon() (mutcleaner.core.codon.CodonTable method) (mutcleaner.core.CodonTable method) is_synonymous() (mutcleaner.core.mutation.AminoAcidMutation method) is_valid_char() (mutcleaner.core.alphabet.BaseAlphabet method) is_valid_sequence() (mutcleaner.core.alphabet.BaseAlphabet method) is_zero_based (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute)

L

label_columns (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup4_cleaner.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup5_cleaner.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig attribute) (mutcleaner.cleaners.TrpBCleanerConfig attribute)

library_sequences (mutcleaner.cleaners.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup5_cleaner.ArchStabMS1E10CleanerSup5Config attribute) list_datasets_with_built_in_cleaners() (in module mutcleaner.utils) (in module mutcleaner.utils.data_source) list_reference_sequences() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) load() (mutcleaner.core.dataset.MutationDataset class method) (mutcleaner.core.MutationDataset class method) (mutcleaner.core.Pipeline class method) (mutcleaner.core.pipeline.Pipeline class method) load_by_reference() (mutcleaner.core.dataset.MutationDataset class method) (mutcleaner.core.MutationDataset class method) load_sequences() (in module mutcleaner.utils.sequence_io) load_structured_data() (mutcleaner.core.Pipeline class method) (mutcleaner.core.pipeline.Pipeline class method)

M

make_resolver() (in module mutcleaner.utils.label_resolvers) map_ambler_positions() (in module mutcleaner.cleaners.ctxm_custom_cleaner) mark_wild_type_in_mut_info() (in module mutcleaner.cleaners.rbd_custom_cleaner) merge() (mutcleaner.cleaners.base_config.BaseCleanerConfig method) merge_columns() (in module mutcleaner.cleaners.basic_cleaners) MGnifyddGCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.mgnify_ddg_cleaner) module mutcleaner.cleaners mutcleaner.cleaners.antitoxin_pard3_cleaner mutcleaner.cleaners.antitoxin_pard3_custom_cleaners mutcleaner.cleaners.archstabms_1e10_custom_cleaners mutcleaner.cleaners.archstabms_1e10_sup4_cleaner mutcleaner.cleaners.archstabms_1e10_sup5_cleaner mutcleaner.cleaners.base_config mutcleaner.cleaners.basic_cleaners mutcleaner.cleaners.cdna_proteolysis_cleaner mutcleaner.cleaners.cdna_proteolysis_custom_cleaners mutcleaner.cleaners.chitosanase_dtm_cleaner mutcleaner.cleaners.chitosanase_dtm_custom_cleaner mutcleaner.cleaners.codon_cdna_proteolysis_cleaner mutcleaner.cleaners.ctxm_cleaner mutcleaner.cleaners.ctxm_custom_cleaner mutcleaner.cleaners.ddg_dtm_cleaners mutcleaner.cleaners.human_domainome_custom_cleaners mutcleaner.cleaners.human_domainome_sup2_cleaner mutcleaner.cleaners.human_domainome_sup4_cleaner mutcleaner.cleaners.human_myoglobin_cleaner mutcleaner.cleaners.human_myoglobin_custom_cleaners mutcleaner.cleaners.mgnify_ddg_cleaner mutcleaner.cleaners.proteingym_dms_substitutions_cleaner mutcleaner.cleaners.proteingym_dms_substitutions_custom_cleaners mutcleaner.cleaners.rbd_ace2_cleaner mutcleaner.cleaners.rbd_antibody_cleaner mutcleaner.cleaners.rbd_custom_cleaner mutcleaner.cleaners.trpb_cleaner mutcleaner.core mutcleaner.core.alphabet mutcleaner.core.codon mutcleaner.core.constants mutcleaner.core.dataset mutcleaner.core.mutation mutcleaner.core.pipeline mutcleaner.core.sequence mutcleaner.core.types mutcleaner.utils mutcleaner.utils.cleaner_workers mutcleaner.utils.data_source mutcleaner.utils.dataset_builders mutcleaner.utils.label_resolvers mutcleaner.utils.mutation_converter mutcleaner.utils.raw_data_downloader mutcleaner.utils.sequence_io mutcleaner.utils.type_converter multiout_step() (in module mutcleaner.core) (in module mutcleaner.core.pipeline) mutation_subtype (mutcleaner.core.mutation.MutationSet property) MutationDataset (class in mutcleaner.core) (class in mutcleaner.core.dataset) MutationSet (class in mutcleaner.core.mutation) mutcleaner.cleaners module mutcleaner.cleaners.antitoxin_pard3_cleaner module mutcleaner.cleaners.antitoxin_pard3_custom_cleaners module mutcleaner.cleaners.archstabms_1e10_custom_cleaners module mutcleaner.cleaners.archstabms_1e10_sup4_cleaner module mutcleaner.cleaners.archstabms_1e10_sup5_cleaner module mutcleaner.cleaners.base_config module mutcleaner.cleaners.basic_cleaners module

mutcleaner.cleaners.cdna_proteolysis_cleaner module mutcleaner.cleaners.cdna_proteolysis_custom_cleaners module mutcleaner.cleaners.chitosanase_dtm_cleaner module mutcleaner.cleaners.chitosanase_dtm_custom_cleaner module mutcleaner.cleaners.codon_cdna_proteolysis_cleaner module mutcleaner.cleaners.ctxm_cleaner module mutcleaner.cleaners.ctxm_custom_cleaner module mutcleaner.cleaners.ddg_dtm_cleaners module mutcleaner.cleaners.human_domainome_custom_cleaners module mutcleaner.cleaners.human_domainome_sup2_cleaner module mutcleaner.cleaners.human_domainome_sup4_cleaner module mutcleaner.cleaners.human_myoglobin_cleaner module mutcleaner.cleaners.human_myoglobin_custom_cleaners module mutcleaner.cleaners.mgnify_ddg_cleaner module mutcleaner.cleaners.proteingym_dms_substitutions_cleaner module mutcleaner.cleaners.proteingym_dms_substitutions_custom_cleaners module mutcleaner.cleaners.rbd_ace2_cleaner module mutcleaner.cleaners.rbd_antibody_cleaner module mutcleaner.cleaners.rbd_custom_cleaner module mutcleaner.cleaners.trpb_cleaner module mutcleaner.core module mutcleaner.core.alphabet module mutcleaner.core.codon module mutcleaner.core.constants module mutcleaner.core.dataset module mutcleaner.core.mutation module mutcleaner.core.pipeline module mutcleaner.core.sequence module mutcleaner.core.types module mutcleaner.utils module mutcleaner.utils.cleaner_workers module mutcleaner.utils.data_source module mutcleaner.utils.dataset_builders module mutcleaner.utils.label_resolvers module mutcleaner.utils.mutation_converter module mutcleaner.utils.raw_data_downloader module mutcleaner.utils.sequence_io module mutcleaner.utils.type_converter module

N

nearest_by (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.MGnifyddGCleanerConfig attribute) normalize_type_conversions() (in module mutcleaner.utils.type_converter)

nucleotide_end (mutcleaner.core.mutation.CodonMutation property) nucleotide_start (mutcleaner.core.mutation.CodonMutation property) num_workers (mutcleaner.cleaners.base_config.BaseCleanerConfig attribute) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig attribute) (mutcleaner.cleaners.TrpBCleanerConfig attribute)

P

parse_chitosanase_raw_file() (in module mutcleaner.cleaners.chitosanase_dtm_custom_cleaner) parse_custom_delimiter_header() (in module mutcleaner.utils.sequence_io) parse_fasta() (in module mutcleaner.utils.sequence_io) parse_ncbi_header() (in module mutcleaner.utils.sequence_io) parse_simple_header() (in module mutcleaner.utils.sequence_io) parse_uniprot_header() (in module mutcleaner.utils.sequence_io) peek() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) Pipeline (class in mutcleaner.core) (class in mutcleaner.core.pipeline) pipeline_name (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup4_cleaner.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup5_cleaner.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.base_config.BaseCleanerConfig attribute) (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.chitosanase_dtm_cleaner.ChitosanasedTmCleanerConfig attribute) (mutcleaner.cleaners.ChitosanasedTmCleanerConfig attribute) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig attribute) (mutcleaner.cleaners.TrpBCleanerConfig attribute) pipeline_step() (in module mutcleaner.core) (in module mutcleaner.core.pipeline) primary_label_column (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup4_cleaner.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup5_cleaner.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig attribute) (mutcleaner.cleaners.TrpBCleanerConfig attribute)

process_domain_positions() (in module mutcleaner.cleaners.human_domainome_custom_cleaners) process_workers (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) ProteinAlphabet (class in mutcleaner.core) (class in mutcleaner.core.alphabet) ProteinGymCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.proteingym_dms_substitutions_cleaner) ProteinSequence (class in mutcleaner.core) (class in mutcleaner.core.sequence)

R

RBDACE2CleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.rbd_ace2_cleaner) RBDAntibodyCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.rbd_antibody_cleaner) read_dataset() (in module mutcleaner.cleaners.basic_cleaners) read_proteingym_dms_substitutions_data() (in module mutcleaner.cleaners.proteingym_dms_substitutions_custom_cleaners) reference_sequences (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) remap_mutation_positions_by_name() (in module mutcleaner.cleaners.basic_cleaners) remove_delayed_step() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) remove_mutation() (mutcleaner.core.mutation.MutationSet method)

remove_mutation_set() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) remove_reference_sequence() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) replace_in_column() (in module mutcleaner.cleaners.basic_cleaners) require_known_reference_sequence (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) reverse_complement() (mutcleaner.core.DNASequence method) (mutcleaner.core.RNASequence method) (mutcleaner.core.sequence.DNASequence method) (mutcleaner.core.sequence.RNASequence method) RNAAlphabet (class in mutcleaner.core) (class in mutcleaner.core.alphabet) RNASequence (class in mutcleaner.core) (class in mutcleaner.core.sequence)

S

save() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) save_artifacts() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) save_by_reference() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) save_structured_data() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) seq_type (mutcleaner.core.CodonMutationSet property) (mutcleaner.core.mutation.CodonMutationSet property) sequence_source (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute)

set_mutation_set_label() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) set_mutation_set_reference() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) show_download_instructions() (in module mutcleaner.utils) (in module mutcleaner.utils.data_source) simplify_mutations() (in module mutcleaner.cleaners.antitoxin_pard3_custom_cleaners) sort_by_position() (mutcleaner.core.mutation.MutationSet method) split_columns() (in module mutcleaner.cleaners.basic_cleaners) standardize_rbd_target_names() (in module mutcleaner.cleaners.rbd_custom_cleaner) store() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) structured_data (mutcleaner.core.Pipeline property) (mutcleaner.core.pipeline.Pipeline property) subtract_labels_by_wt() (in module mutcleaner.cleaners.basic_cleaners)

T

target_name_aliases (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) then() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) to_amino_acid_mutation() (mutcleaner.core.mutation.CodonMutation method) to_amino_acid_mutation_set() (mutcleaner.core.CodonMutationSet method) (mutcleaner.core.mutation.CodonMutationSet method) to_dataframe() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) to_dict() (mutcleaner.cleaners.base_config.BaseCleanerConfig method) to_json() (mutcleaner.cleaners.base_config.BaseCleanerConfig method) transcribe() (mutcleaner.core.DNASequence method) (mutcleaner.core.sequence.DNASequence method) transform() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method) translate() (mutcleaner.core.DNASequence method) (mutcleaner.core.RNASequence method) (mutcleaner.core.sequence.DNASequence method) (mutcleaner.core.sequence.RNASequence method) translate_codon() (mutcleaner.core.codon.CodonTable method) (mutcleaner.core.CodonTable method) TrpBCleanerConfig (class in mutcleaner.cleaners) (class in mutcleaner.cleaners.trpb_cleaner) type (mutcleaner.core.mutation.AminoAcidMutation property) (mutcleaner.core.mutation.BaseMutation property) (mutcleaner.core.mutation.CodonMutation property) type_conversions (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup4_cleaner.ArchStabMS1E10CleanerSup4Config attribute) (mutcleaner.cleaners.archstabms_1e10_sup5_cleaner.ArchStabMS1E10CleanerSup5Config attribute) (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.DdgDtmCleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.MGnifyddGCleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig attribute) (mutcleaner.cleaners.TrpBCleanerConfig attribute)

V

valid_single_mutation() (in module mutcleaner.utils.cleaner_workers) validate() (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig method) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig method) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup4Config method) (mutcleaner.cleaners.ArchStabMS1E10CleanerSup5Config method) (mutcleaner.cleaners.archstabms_1e10_sup4_cleaner.ArchStabMS1E10CleanerSup4Config method) (mutcleaner.cleaners.archstabms_1e10_sup5_cleaner.ArchStabMS1E10CleanerSup5Config method) (mutcleaner.cleaners.base_config.BaseCleanerConfig method) (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig method) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig method) (mutcleaner.cleaners.chitosanase_dtm_cleaner.ChitosanasedTmCleanerConfig method) (mutcleaner.cleaners.ChitosanasedTmCleanerConfig method) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig method) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig method) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig method) (mutcleaner.cleaners.CTXMCleanerConfig method) (mutcleaner.cleaners.ddg_dtm_cleaners.DdgDtmCleanerConfig method) (mutcleaner.cleaners.DdgDtmCleanerConfig method) (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig method) (mutcleaner.cleaners.human_domainome_sup4_cleaner.HumanDomainomeSup4CleanerConfig method) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig method) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig method) (mutcleaner.cleaners.HumanDomainomeSup4CleanerConfig method) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig method) (mutcleaner.cleaners.mgnify_ddg_cleaner.MGnifyddGCleanerConfig method) (mutcleaner.cleaners.MGnifyddGCleanerConfig method) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig method) (mutcleaner.cleaners.ProteinGymCleanerConfig method) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig method) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig method) (mutcleaner.cleaners.RBDACE2CleanerConfig method) (mutcleaner.cleaners.RBDAntibodyCleanerConfig method) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig method) (mutcleaner.cleaners.TrpBCleanerConfig method) (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method)

validate_against_references() (mutcleaner.core.dataset.MutationDataset method) (mutcleaner.core.MutationDataset method) validate_all() (mutcleaner.core.mutation.MutationSet method) validate_config (mutcleaner.cleaners.base_config.BaseCleanerConfig attribute) validate_mut_workers (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.rbd_ace2_cleaner.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.rbd_antibody_cleaner.RBDAntibodyCleanerConfig attribute) (mutcleaner.cleaners.RBDACE2CleanerConfig attribute) (mutcleaner.cleaners.RBDAntibodyCleanerConfig attribute) validate_mutations() (in module mutcleaner.cleaners.basic_cleaners) validate_sequence() (mutcleaner.core.alphabet.BaseAlphabet method) validate_single_mutation_and_sequence() (in module mutcleaner.utils.cleaner_workers) validate_wt_sequence() (in module mutcleaner.cleaners.cdna_proteolysis_custom_cleaners) validate_wt_workers (mutcleaner.cleaners.cdna_proteolysis_cleaner.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.codon_cdna_proteolysis_cleaner.CodoncDNAProteolysisCleanerConfig attribute) (mutcleaner.cleaners.CodoncDNAProteolysisCleanerConfig attribute) validation_workers (mutcleaner.cleaners.human_domainome_sup2_cleaner.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.HumanDomainomeSup2CleanerConfig attribute) (mutcleaner.cleaners.proteingym_dms_substitutions_cleaner.ProteinGymCleanerConfig attribute) (mutcleaner.cleaners.ProteinGymCleanerConfig attribute) visualize_pipeline() (mutcleaner.core.Pipeline method) (mutcleaner.core.pipeline.Pipeline method)

W

write_fasta() (in module mutcleaner.utils.sequence_io) wt_name (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) wt_separator (mutcleaner.cleaners.chitosanase_dtm_cleaner.ChitosanasedTmCleanerConfig attribute) (mutcleaner.cleaners.ChitosanasedTmCleanerConfig attribute) wt_sequence (mutcleaner.cleaners.antitoxin_pard3_cleaner.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.AntitoxinParD3CleanerConfig attribute) (mutcleaner.cleaners.ctxm_cleaner.CTXMCleanerConfig attribute) (mutcleaner.cleaners.CTXMCleanerConfig attribute) (mutcleaner.cleaners.human_myoglobin_cleaner.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.HumanMyoglobinCleanerConfig attribute) (mutcleaner.cleaners.trpb_cleaner.TrpBCleanerConfig attribute) (mutcleaner.cleaners.TrpBCleanerConfig attribute)