Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Y | Z A affinity_model() (mhcmatch.store.Store method) affinity_nm (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) affinity_rank (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) AffinityModel (class in mhcmatch.affinity) aggregate() (in module mhcmatch.rank) AGGREGATE_ARTIFACTS (in module mhcmatch.rank) AGGREGATE_BLOCKS (in module mhcmatch.rank) AGGREGATE_COLUMNS (in module mhcmatch.rank) AGGREGATE_FEATURES (in module mhcmatch.rank) aggregate_features() (in module mhcmatch.rank) AGGREGATE_MODES (in module mhcmatch.rank) aggregate_score() (in module mhcmatch.rank) AGGREGATE_VARIANTS (in module mhcmatch.rank) agretopicity (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) allele (mhcmatch.mimics.MimicResult attribute) (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) (mhcmatch.store.Restriction attribute) (mhcmatch.vector.Feature attribute) (mhcmatch.vector.Unit attribute) allele_scored (mhcmatch.rank.Ranked attribute) alleles() (mhcmatch.store.Store method) alleles_presenting (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) alpha_prior() (in module mhcmatch.pseudoseq) amplitude (mhcmatch.predict.Prediction attribute) amplitude() (mhcmatch.affinity.AffinityModel method) (mhcmatch.affinity.PottsAffinity method) anchor_indices() (in module mhcmatch.store) anchor_model() (mhcmatch.store.Store method) anchor_preferences() (mhcmatch.store.Store method) ANCHOR_SCHEMES (in module mhcmatch.immuno) anchor_score (mhcmatch.store.Restriction attribute) anchor_terms() (mhcmatch.diffusion.AnchorModel method) (mhcmatch.diffusion.RoutedAnchorModel method) AnchorModel (class in mhcmatch.diffusion) ANCHORS (in module mhcmatch.complement) (in module mhcmatch.posbayes) anchors (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Decomposition attribute) annotate() (in module mhcmatch.mimicry) ANNOTATE_COLUMNS (in module mhcmatch.rank) anticore (mhcmatch.diffusion.AnchorModel attribute) anticore_w (mhcmatch.diffusion.AnchorModel attribute) apply_log_odds() (in module mhcmatch.complement) arms (mhcmatch.portfolio.Composition attribute) as_dict() (mhcmatch.mimicry.MimicryScore method) as_keep() (in module mhcmatch.predict) as_rna() (mhcmatch.vector.MRNA method) ASSAY_FLANK (in module mhcmatch.ligand) assemble() (in module mhcmatch.vector) assign_genes() (mhcmatch.proteome.Proteome method) autoimmune (mhcmatch.mimicry.MimicryScore attribute) B back_translate() (in module mhcmatch.vector) background (mhcmatch.ligand.SpanModel attribute) band (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Restriction attribute) band() (in module mhcmatch.calibrate) band_for() (in module mhcmatch.predict) BASE_COLUMNS (in module mhcmatch.rank) batch_scale() (in module mhcmatch.expression) best_register() (mhcmatch.diffusion.AnchorModel method) (mhcmatch.diffusion.RoutedAnchorModel method) best_span() (mhcmatch.ligand.SpanModel method) betabinom_rho() (in module mhcmatch.portfolio) binder (mhcmatch.mimics.MimicResult attribute) (mhcmatch.rank.Ranked attribute) (mhcmatch.store.Restriction attribute) binder_band (mhcmatch.predict.Prediction attribute) binder_rank (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) binder_ranks() (in module mhcmatch.predict) binder_score() (in module mhcmatch.predict) (mhcmatch.store.Store method) BinderScore (class in mhcmatch.predict) binding_core() (in module mhcmatch.store) block_live (mhcmatch.cassette.Cassette attribute) BLOCKS (in module mhcmatch.complement) blocks() (in module mhcmatch.complement) BLOCKS_MHC2 (in module mhcmatch.complement) BLOSUM62_BG (in module mhcmatch.pseudoseq) blosum62_conditional() (in module mhcmatch.pseudoseq) boundaries (mhcmatch.vector.Cassette attribute) build_axes() (in module mhcmatch.cassette) build_scorer() (in module mhcmatch.predict) burial() (in module mhcmatch.complement) C C_MAX (in module mhcmatch.expression) C_MIN (in module mhcmatch.expression) CACHE_DEFAULT (in module mhcmatch.calibrate) cache_dir() (in module mhcmatch.calibrate) CACHE_ENV (in module mhcmatch.calibrate) CANONICAL_LEN (in module mhcmatch.mimics) Cassette (class in mhcmatch.cassette) (class in mhcmatch.vector) category (mhcmatch.mimics.MimicResult attribute) cds (mhcmatch.vector.MRNA attribute) CHANNEL_COLUMNS (in module mhcmatch.rank) CHANNELS (in module mhcmatch.mimicry) channels (mhcmatch.cassette.Cassette attribute) chebyshev_score() (in module mhcmatch.portfolio) checks (mhcmatch.vector.MRNA property) class2_from_name() (in module mhcmatch.pseudoseq) class2_key() (in module mhcmatch.pseudoseq) class2_report() (in module mhcmatch.pseudoseq) CLASSES (in module mhcmatch.complement) clear() (mhcmatch.calibrate.RankCalibrator method) clipped (mhcmatch.ligand.Span attribute) cls (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.vector.Feature attribute) (mhcmatch.vector.Linker attribute) (mhcmatch.vector.Unit attribute) CLS_REFS (in module mhcmatch.mimics) cluster() (mhcmatch.pseudoseq.Pseudoseq method) CODON_USAGE_HUMAN (in module mhcmatch.vector) coexpression() (in module mhcmatch.expression) COLUMNS (in module mhcmatch.expression) columns() (in module mhcmatch.rank) COMPONENTS (in module mhcmatch.mimicry) components (mhcmatch.mimicry.MimicryScore attribute) (mhcmatch.rank.Ranked attribute) compose() (in module mhcmatch.portfolio) Composition (class in mhcmatch.portfolio) contact_profile() (in module mhcmatch.immuno) context_floor() (in module mhcmatch.expression) context_score() (mhcmatch.ligand.SpanModel method) contract() (in module mhcmatch.mimicry) core (mhcmatch.ligand.Span attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) (mhcmatch.vector.Feature attribute) CORE_COLUMNS (in module mhcmatch.predict) core_end (mhcmatch.vector.Feature attribute) CORE_LEN (in module mhcmatch.store) core_offset (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) core_source (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) core_start (mhcmatch.ligand.Span attribute) (mhcmatch.vector.Feature attribute) corner() (in module mhcmatch.portfolio) corpus_counts() (in module mhcmatch.mimicry) CORPUS_K (in module mhcmatch.mimicry) corpus_R() (in module mhcmatch.mimicry) CORPUS_REFERENCE (in module mhcmatch.mimicry) corpus_shapes() (in module mhcmatch.mimicry) corpus_spectrum() (in module mhcmatch.mimicry) corpus_stats() (in module mhcmatch.calibrate) cost (mhcmatch.vector.Cassette attribute) counts_by_distance() (in module mhcmatch.luksza) coverage (mhcmatch.cassette.Cassette attribute) (mhcmatch.portfolio.Composition attribute) coverage() (in module mhcmatch.portfolio) crowding_distance() (in module mhcmatch.portfolio) ctx (mhcmatch.ligand.SpanModel attribute) CTX_KEYS (in module mhcmatch.ligand) D d_occupancy (mhcmatch.rank.Ranked attribute) dai (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked property) dai() (mhcmatch.affinity.AffinityModel method) (mhcmatch.affinity.PottsAffinity method) ddg() (mhcmatch.structure.StructureScorer method) decompose() (mhcmatch.store.Store method) Decomposition (class in mhcmatch.store) default_head() (in module mhcmatch.recognition) DEFAULT_REFS (in module mhcmatch.mimics) DEFAULT_SCALES (in module mhcmatch.immuno) density (mhcmatch.mimicry.MimicryScore attribute) DESCRIPTOR_PREFIX (in module mhcmatch.data.aa_tables) DESCRIPTORS (in module mhcmatch.data.aa_tables) design() (in module mhcmatch.complement) (in module mhcmatch.recognition) deslip() (in module mhcmatch.vector) dispersion() (in module mhcmatch.portfolio) diversity (mhcmatch.cassette.Cassette attribute) diversity() (in module mhcmatch.cassette) dropped (mhcmatch.vector.Selection attribute) E e_value (mhcmatch.mimics.MimicResult attribute) embed() (in module mhcmatch.recognition) encode() (in module mhcmatch.complement) end (mhcmatch.ligand.Span attribute) (mhcmatch.vector.Feature attribute) energy (mhcmatch.cassette.Cassette attribute) enrichment (mhcmatch.store.Restriction attribute) epitope_map() (in module mhcmatch.vector) escape (mhcmatch.cassette.Cassette attribute) ESSENTIAL_TISSUES (in module mhcmatch.vector) expected_yield (mhcmatch.vector.Selection property) EXPR_COLUMNS (in module mhcmatch.rank) expr_norm_level() (in module mhcmatch.rank) expr_pct (mhcmatch.rank.Ranked attribute) expr_percentile() (in module mhcmatch.rank) expression (mhcmatch.rank.Ranked attribute) expression_imputed (mhcmatch.rank.Ranked attribute) EXTENDED_COLUMNS (in module mhcmatch.rank) EXTENDED_LEN (in module mhcmatch.mimics) F face_kmers() (in module mhcmatch.mimicry) family (mhcmatch.vector.Linker attribute) Feature (class in mhcmatch.vector) feature_names() (in module mhcmatch.complement) (in module mhcmatch.immuno) (in module mhcmatch.recognition) features() (in module mhcmatch.complement) (in module mhcmatch.immuno) (in module mhcmatch.mimicry) (mhcmatch.affinity.AffinityModel method) FEATURES_ONLY (in module mhcmatch.rank) FEATURES_ONLY_PATHOGEN (in module mhcmatch.rank) fetch_file() (in module mhcmatch.store) fetch_matrix() (in module mhcmatch.expression) fetch_pmhc() (in module mhcmatch.store) fetch_proteome() (in module mhcmatch.store) fetch_reference() (in module mhcmatch.expression) fetch_synonyms() (in module mhcmatch.expression) find_exact_sources() (mhcmatch.proteome.Proteome method) find_source() (mhcmatch.proteome.Proteome method) find_sources() (mhcmatch.proteome.Proteome method) fit() (mhcmatch.affinity.AffinityModel method) fit_ridge() (in module mhcmatch.affinity) FITTED (in module mhcmatch.complement) fitted() (in module mhcmatch.complement) FITTED_HEADS (in module mhcmatch.recognition) FITTED_MHC2 (in module mhcmatch.complement) fixed_span() (in module mhcmatch.ligand) flank_identity() (in module mhcmatch.vector) FLANK_KEYS (in module mhcmatch.ligand) flanks (mhcmatch.ligand.Span property) FLOORS_FILE (in module mhcmatch.expression) FLOORS_FILE_MOUSE (in module mhcmatch.expression) from_fasta() (mhcmatch.proteome.Proteome class method) from_hf() (mhcmatch.proteome.Proteome class method) from_pmhc() (mhcmatch.store.Store class method) from_records() (mhcmatch.store.Store class method) from_sequence() (in module mhcmatch.vector) G GAMMA (in module mhcmatch.cassette) gamma (mhcmatch.cassette.Cassette attribute) GAMMA_MAX (in module mhcmatch.expression) GAMMA_MIN (in module mhcmatch.expression) GATE (in module mhcmatch.rank) gate_probability() (in module mhcmatch.rank) gene (mhcmatch.rank.Ranked attribute) (mhcmatch.vector.Feature attribute) (mhcmatch.vector.Unit attribute) gene_level() (in module mhcmatch.expression) gene_symbols() (in module mhcmatch.proteome) genes (mhcmatch.predict.Keep attribute) goal_energy() (in module mhcmatch.cassette) greedy() (in module mhcmatch.cassette) group_offsets() (in module mhcmatch.cassette) H HEADS (in module mhcmatch.recognition) hla_spellings() (in module mhcmatch.pseudoseq) how (mhcmatch.cassette.Cassette attribute) HUMAN (in module mhcmatch.posbayes) HYDROPHOBICITY (in module mhcmatch.data.aa_tables) I ic50_to_y() (in module mhcmatch.affinity) id (mhcmatch.vector.Feature attribute) impute() (in module mhcmatch.expression) imputed (mhcmatch.rank.Ranked attribute) index (mhcmatch.cassette.Cassette attribute) (mhcmatch.predict.Keep attribute) infer_class() (in module mhcmatch.store) is_binder() (mhcmatch.store.Store method) is_kept() (in module mhcmatch.predict) is_presented() (mhcmatch.store.Store method) J joint (mhcmatch.portfolio.Composition property) JUNCTION_LENGTHS (in module mhcmatch.vector) junction_windows() (in module mhcmatch.vector) junctions (mhcmatch.vector.Cassette attribute) K k (mhcmatch.cassette.Cassette attribute) KAPPA (in module mhcmatch.cassette) KD_THRESHOLD (in module mhcmatch.complement) Keep (class in mhcmatch.predict) keep (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) KEEP_BUILTIN (in module mhcmatch.predict) KEEP_COLUMN (in module mhcmatch.predict) keep_epitope_index() (in module mhcmatch.predict) keep_genes() (in module mhcmatch.predict) KEEP_INDEX_FILE (in module mhcmatch.predict) keep_reason (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) KEEP_REASON_COLUMN (in module mhcmatch.predict) KEEP_REASONS (in module mhcmatch.predict) keep_set() (in module mhcmatch.predict) kernel() (mhcmatch.pseudoseq.Pseudoseq method) keys (mhcmatch.vector.Selection attribute) kidera_design() (in module mhcmatch.complement) kidera_names() (in module mhcmatch.complement) kind (mhcmatch.vector.Feature attribute) (mhcmatch.vector.Unit attribute) KINDS (in module mhcmatch.mimics) KMER (in module mhcmatch.cassette) KMER_LENS (in module mhcmatch.predict) known_epitope (mhcmatch.rank.Ranked attribute) L lam (mhcmatch.cassette.Cassette attribute) lam() (in module mhcmatch.cassette) learn_anchor_weights() (in module mhcmatch.pseudoseq) length (mhcmatch.vector.Feature property) length_bin() (in module mhcmatch.complement) LENGTH_BINS (in module mhcmatch.complement) length_logodds() (mhcmatch.diffusion.AnchorModel method) length_preferences() (mhcmatch.store.Store method) length_range() (in module mhcmatch.mimics) lens (mhcmatch.ligand.SpanModel attribute) LIGAND_KEYS (in module mhcmatch.ligand) LIGAND_LENGTHS (in module mhcmatch.store) linearly_supported() (in module mhcmatch.portfolio) Linker (class in mhcmatch.vector) linker (mhcmatch.vector.MRNA attribute) LINKERS (in module mhcmatch.vector) llr() (in module mhcmatch.posbayes) load() (in module mhcmatch.expression) (in module mhcmatch.known) (mhcmatch.affinity.AffinityModel class method) load_markov1() (in module mhcmatch.diffusion) load_peptides() (in module mhcmatch.mimics) load_pseudo() (in module mhcmatch.pseudoseq) load_reference_sets() (in module mhcmatch.mimics) load_references() (in module mhcmatch.mimicry) load_span_model() (in module mhcmatch.ligand) load_vendored_anchor_model() (in module mhcmatch.diffusion) LOCUS_W (in module mhcmatch.mimicry) locus_weights() (in module mhcmatch.mimicry) log_ek() (in module mhcmatch.cassette) log_odds_table() (in module mhcmatch.recognition) logodds (mhcmatch.mimicry.MimicryScore attribute) lookup() (in module mhcmatch.expression) (in module mhcmatch.known) lowest_bic_head() (in module mhcmatch.recognition) M MAP_COLUMNS (in module mhcmatch.vector) map_rows() (in module mhcmatch.vector) map_summary() (in module mhcmatch.vector) MarginalExceedsBlock masks() (in module mhcmatch.mimicry) Match (class in mhcmatch.search) matched_tissues() (in module mhcmatch.expression) MATRIX_FILE (in module mhcmatch.expression) matrix_file() (in module mhcmatch.expression) MATRIX_FILE_MOUSE (in module mhcmatch.expression) MAX_HOMOPOLYMER (in module mhcmatch.vector) MAX_POOL (in module mhcmatch.cassette) mhc1_positions() (in module mhcmatch.store) MHC2_ANCHORS (in module mhcmatch.recognition) mhc2_anchors() (in module mhcmatch.complement) mhc2_core() (in module mhcmatch.recognition) MHC2_JUNCTION_LENGTHS (in module mhcmatch.vector) MHC2_LEN_EDGES (in module mhcmatch.complement) mhc2_length_bin() (in module mhcmatch.complement) MHC2_MAP_LENGTHS (in module mhcmatch.vector) MHC2_ZONES (in module mhcmatch.complement) mhcmatch.affinity module mhcmatch.calibrate module mhcmatch.cassette module mhcmatch.complement module mhcmatch.data.aa_tables module mhcmatch.data.contact_profile module mhcmatch.diffusion module mhcmatch.expression module mhcmatch.immuno module mhcmatch.known module mhcmatch.ligand module mhcmatch.logo module mhcmatch.luksza module mhcmatch.mimicry module mhcmatch.mimics module mhcmatch.portfolio module mhcmatch.posbayes module mhcmatch.predict module mhcmatch.proteome module mhcmatch.pseudoseq module mhcmatch.rank module mhcmatch.recognition module mhcmatch.search module mhcmatch.store module mhcmatch.structure module mhcmatch.vector module MimicResult (class in mhcmatch.mimics) MIMICRY_PAIRS (in module mhcmatch.rank) MimicryScore (class in mhcmatch.mimicry) MIN_COVERAGE (in module mhcmatch.expression) MIN_SHARED (in module mhcmatch.expression) mismatch (mhcmatch.predict.Keep attribute) mj_energies() (mhcmatch.structure.StructureScorer method) mj_energy() (mhcmatch.structure.StructureScorer method) MJ_PARTITION (in module mhcmatch.data.aa_tables) model_peptide (mhcmatch.predict.Prediction attribute) models() (in module mhcmatch.rank) module mhcmatch.affinity mhcmatch.calibrate mhcmatch.cassette mhcmatch.complement mhcmatch.data.aa_tables mhcmatch.data.contact_profile mhcmatch.diffusion mhcmatch.expression mhcmatch.immuno mhcmatch.known mhcmatch.ligand mhcmatch.logo mhcmatch.luksza mhcmatch.mimicry mhcmatch.mimics mhcmatch.portfolio mhcmatch.posbayes mhcmatch.predict mhcmatch.proteome mhcmatch.pseudoseq mhcmatch.rank mhcmatch.recognition mhcmatch.search mhcmatch.store mhcmatch.structure mhcmatch.vector motif() (in module mhcmatch.logo) MOUSE (in module mhcmatch.posbayes) MRNA (class in mhcmatch.vector) mrna() (in module mhcmatch.vector) mutation_index (mhcmatch.vector.Unit attribute) mutations (mhcmatch.proteome.SourceHit attribute) mutual_information() (in module mhcmatch.pseudoseq) N n0 (mhcmatch.vector.Selection attribute) n_alleles_presenting (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) n_alternatives (mhcmatch.ligand.Span attribute) n_composite (mhcmatch.cassette.Cassette attribute) n_effective() (in module mhcmatch.portfolio) n_exact (mhcmatch.mimics.MimicResult attribute) n_hits (mhcmatch.mimics.MimicResult attribute) n_near (mhcmatch.mimics.MimicResult attribute) n_subs (mhcmatch.proteome.SourceHit attribute) n_unresolved (mhcmatch.cassette.Cassette attribute) n_votes (mhcmatch.store.Restriction attribute) name (mhcmatch.vector.Linker attribute) NATIVE_COLUMNS (in module mhcmatch.predict) NATIVE_CORPUS_COMPONENTS (in module mhcmatch.mimicry) nearest (mhcmatch.mimicry.MimicryScore attribute) neighbors() (mhcmatch.pseudoseq.Pseudoseq method) neighbours() (in module mhcmatch.mimics) NEOAG_COLUMNS (in module mhcmatch.mimicry) nondominated_rank() (in module mhcmatch.portfolio) normalise_axes() (in module mhcmatch.cassette) normalize_allele() (in module mhcmatch.pseudoseq) not_worse (mhcmatch.cassette.Cassette attribute) not_worse() (in module mhcmatch.cassette) note (mhcmatch.vector.Linker attribute) NOVEL_PRODUCTS (in module mhcmatch.predict) O observed_spans() (in module mhcmatch.ligand) occupancy (mhcmatch.rank.Ranked attribute) of_kind() (mhcmatch.vector.MRNA method) offset (mhcmatch.cassette.Cassette attribute) (mhcmatch.predict.Prediction attribute) offtarget_cost() (in module mhcmatch.vector) order() (in module mhcmatch.vector) overlap() (in module mhcmatch.cassette) overlaps (mhcmatch.vector.Feature attribute) P p (mhcmatch.cassette.Cassette attribute) (mhcmatch.vector.Unit attribute) p_at_least() (in module mhcmatch.portfolio) p_binder (mhcmatch.predict.BinderScore attribute) p_present (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Restriction attribute) p_present() (mhcmatch.calibrate.RankCalibrator method) p_response (mhcmatch.rank.Ranked attribute) PAD (in module mhcmatch.ligand) padbg (mhcmatch.ligand.SpanModel attribute) pair_stats() (in module mhcmatch.cassette) panel_alleles() (mhcmatch.store.Store method) panel_key() (mhcmatch.diffusion.AnchorModel method) panel_sha() (in module mhcmatch.diffusion) parameters() (in module mhcmatch.complement) PARAMS (in module mhcmatch.complement) params (mhcmatch.predict.Keep attribute) params() (in module mhcmatch.mimicry) PARATOPE (in module mhcmatch.complement) PARATOPE_CONTACT (in module mhcmatch.complement) pareto_front() (in module mhcmatch.portfolio) parse_fasta() (in module mhcmatch.predict) parse_variant_header() (in module mhcmatch.predict) parts (mhcmatch.vector.MRNA attribute) patient_summary() (in module mhcmatch.mimics) peptide (mhcmatch.ligand.Span attribute) (mhcmatch.mimicry.MimicryScore attribute) (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) (mhcmatch.search.Match attribute) (mhcmatch.store.Decomposition attribute) (mhcmatch.vector.Unit attribute) per_allele() (mhcmatch.vector.Selection method) per_block() (mhcmatch.vector.Selection method) percent_rank (mhcmatch.predict.Prediction attribute) percent_rank() (mhcmatch.calibrate.RankCalibrator method) percent_ranks() (mhcmatch.store.Store method) PHYS_COLUMNS (in module mhcmatch.rank) PHYS_SCALE (in module mhcmatch.complement) phys_scale() (in module mhcmatch.complement) physchem (mhcmatch.rank.Ranked attribute) pi (mhcmatch.cassette.Cassette attribute) pool_n (mhcmatch.cassette.Cassette attribute) POOL_PREVALENCE (in module mhcmatch.rank) position (mhcmatch.proteome.SourceHit attribute) position_weights() (in module mhcmatch.immuno) posterior() (in module mhcmatch.complement) (in module mhcmatch.posbayes) (in module mhcmatch.recognition) PottsAffinity (class in mhcmatch.affinity) predict_fasta() (in module mhcmatch.predict) predict_ic50() (mhcmatch.affinity.AffinityModel method) (mhcmatch.affinity.PottsAffinity method) predict_windows() (in module mhcmatch.predict) predict_y() (mhcmatch.affinity.AffinityModel method) (mhcmatch.affinity.PottsAffinity method) predict_y_batch() (mhcmatch.affinity.PottsAffinity method) Prediction (class in mhcmatch.predict) presentation (mhcmatch.rank.Ranked attribute) (mhcmatch.store.Decomposition attribute) presentation_rank (mhcmatch.predict.BinderScore attribute) presentation_sd (mhcmatch.predict.BinderScore attribute) presented() (in module mhcmatch.vector) presented_span() (in module mhcmatch.ligand) prob_offset() (in module mhcmatch.cassette) probability() (in module mhcmatch.mimicry) (in module mhcmatch.rank) processing_score() (in module mhcmatch.ligand) PROPERTY_PC1 (in module mhcmatch.data.aa_tables) PROPERTY_PC2 (in module mhcmatch.data.aa_tables) protein (mhcmatch.proteome.SourceHit attribute) (mhcmatch.vector.MRNA attribute) Proteome (class in mhcmatch.proteome) proteome_peptides() (in module mhcmatch.mimics) PROTEOME_REFS (in module mhcmatch.mimics) proteome_window_array() (in module mhcmatch.mimics) PSEUDO_MATRICES (in module mhcmatch.pseudoseq) Pseudoseq (class in mhcmatch.pseudoseq) R r_term() (in module mhcmatch.luksza) random_peptides() (in module mhcmatch.calibrate) rank (mhcmatch.rank.Ranked attribute) (mhcmatch.store.Restriction attribute) (mhcmatch.vector.Feature attribute) rank_cutoffs() (in module mhcmatch.vector) RANK_DEFAULT_TIER (in module mhcmatch.predict) (in module mhcmatch.vector) rank_fasta() (in module mhcmatch.rank) RANK_NONE (in module mhcmatch.predict) rank_pairs() (in module mhcmatch.rank) RANK_STRONG (in module mhcmatch.predict) rank_table() (in module mhcmatch.rank) RANK_TIERS (in module mhcmatch.predict) RankCalibrator (class in mhcmatch.calibrate) Ranked (class in mhcmatch.rank) read_fasta() (in module mhcmatch.proteome) reason() (mhcmatch.predict.Keep method) reasons() (mhcmatch.predict.Keep method) rebuild() (in module mhcmatch.vector) ref_path() (in module mhcmatch.mimics) ref_peptide (mhcmatch.proteome.SourceHit attribute) REFERENCE_FILE (in module mhcmatch.expression) reference_file() (in module mhcmatch.expression) REFERENCE_FILE_MOUSE (in module mhcmatch.expression) reference_species() (in module mhcmatch.mimicry) REFERENCE_TOIL_FILE (in module mhcmatch.expression) refine() (in module mhcmatch.cassette) register_entropy() (mhcmatch.diffusion.AnchorModel method) render() (in module mhcmatch.logo) REPORT_MODES (in module mhcmatch.pseudoseq) resolve_allele() (in module mhcmatch.pseudoseq) resolve_anchor_index() (in module mhcmatch.store) resolve_context() (in module mhcmatch.expression) resolve_linker() (in module mhcmatch.vector) resolve_rank_threshold() (in module mhcmatch.predict) resolve_restriction() (in module mhcmatch.cassette) Restriction (class in mhcmatch.store) restriction() (mhcmatch.store.Store method) reverse (mhcmatch.diffusion.AnchorModel attribute) reverse_by_allele (mhcmatch.diffusion.AnchorModel attribute) reverse_ctx (mhcmatch.diffusion.AnchorModel attribute) rho (mhcmatch.cassette.Cassette attribute) RHO_ASSAYED (in module mhcmatch.cassette) risk_aversion() (in module mhcmatch.cassette) roles() (in module mhcmatch.posbayes) roles_for() (in module mhcmatch.recognition) RoutedAnchorModel (class in mhcmatch.diffusion) row (mhcmatch.rank.Ranked attribute) rule (mhcmatch.cassette.Cassette attribute) S safety() (in module mhcmatch.mimicry) safety_profile() (in module mhcmatch.expression) save_vendored_anchor_model() (in module mhcmatch.diffusion) scales() (in module mhcmatch.immuno) scan() (in module mhcmatch.mimics) scan_junctions() (in module mhcmatch.vector) scan_protein() (mhcmatch.store.Store method) score (mhcmatch.ligand.Span attribute) (mhcmatch.rank.Ranked attribute) (mhcmatch.search.Match attribute) score() (in module mhcmatch.cassette) (in module mhcmatch.complement) (in module mhcmatch.mimicry) (in module mhcmatch.recognition) (mhcmatch.diffusion.AnchorModel method) (mhcmatch.diffusion.RoutedAnchorModel method) score_many() (mhcmatch.diffusion.AnchorModel method) (mhcmatch.diffusion.RoutedAnchorModel method) score_mhc2() (in module mhcmatch.recognition) score_sd() (mhcmatch.diffusion.AnchorModel method) (mhcmatch.diffusion.RoutedAnchorModel method) SCORED_COLUMNS (in module mhcmatch.predict) SCORER_EPOCH (in module mhcmatch.predict) screen() (in module mhcmatch.vector) search() (in module mhcmatch.search) select() (in module mhcmatch.cassette) (in module mhcmatch.vector) Selection (class in mhcmatch.vector) selectivity (mhcmatch.cassette.Cassette attribute) selectivity_delta() (in module mhcmatch.cassette) self_origin_risk() (in module mhcmatch.vector) seq (mhcmatch.vector.Feature attribute) sequence (mhcmatch.vector.Cassette attribute) (mhcmatch.vector.Linker attribute) (mhcmatch.vector.MRNA attribute) sequence_overlap() (in module mhcmatch.cassette) SET_NAMES (in module mhcmatch.known) shape() (in module mhcmatch.luksza) SHAPES (in module mhcmatch.mimicry) shared_kmers (mhcmatch.search.Match attribute) shrink() (mhcmatch.pseudoseq.Pseudoseq method) significant (mhcmatch.mimics.MimicResult attribute) size_for() (in module mhcmatch.cassette) slice_of() (mhcmatch.vector.MRNA method) slippery_sites() (in module mhcmatch.vector) source (mhcmatch.ligand.Span attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) SourceHit (class in mhcmatch.proteome) SOURCES (in module mhcmatch.known) spacer (mhcmatch.vector.Cassette attribute) SPACERS (in module mhcmatch.vector) Span (class in mhcmatch.ligand) SpanModel (class in mhcmatch.ligand) SPECIES (in module mhcmatch.complement) (in module mhcmatch.expression) species (mhcmatch.store.Store attribute) species_of() (in module mhcmatch.rank) SPECIES_REFS (in module mhcmatch.mimics) split_alleles() (in module mhcmatch.rank) stand_in() (in module mhcmatch.rank) start (mhcmatch.ligand.Span attribute) (mhcmatch.vector.Feature attribute) Store (class in mhcmatch.store) store_binder() (in module mhcmatch.vector) store_ranker() (in module mhcmatch.vector) STRUCTURE_FLANK (in module mhcmatch.ligand) StructureScorer (class in mhcmatch.structure) substitution_conditional() (in module mhcmatch.pseudoseq) support (mhcmatch.ligand.Span attribute) survival() (in module mhcmatch.portfolio) swap_for_diversity() (in module mhcmatch.cassette) swaps (mhcmatch.cassette.Cassette attribute) SYNONYMS_FILE (in module mhcmatch.expression) synth_peptide (mhcmatch.predict.Prediction attribute) T table() (in module mhcmatch.complement) (in module mhcmatch.posbayes) (in module mhcmatch.recognition) TABLES (in module mhcmatch.complement) tcr_face() (in module mhcmatch.cassette) tcr_facing (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Decomposition attribute) TCR_THIRDS (in module mhcmatch.complement) template_for() (mhcmatch.structure.StructureScorer method) TERMS_MHC2_EXPECTED (in module mhcmatch.rank) TERMS_MOUSE_EXPECTED (in module mhcmatch.rank) TERMS_PATHOGEN_EXPECTED (in module mhcmatch.rank) threads (mhcmatch.predict.Keep attribute) tile() (in module mhcmatch.predict) tissues() (in module mhcmatch.expression) top_mimic (mhcmatch.mimics.MimicResult attribute) top_subs (mhcmatch.mimics.MimicResult attribute) trace (mhcmatch.portfolio.Composition attribute) (mhcmatch.vector.Selection attribute) TRACT_PRODUCTS (in module mhcmatch.predict) translate() (in module mhcmatch.vector) trim_allele() (in module mhcmatch.pseudoseq) trimmed (mhcmatch.cassette.Cassette attribute) TUMOR_FILE_MOUSE (in module mhcmatch.expression) TUMOR_TISSUE (in module mhcmatch.expression) TUMOR_TISSUE_APPROXIMATE (in module mhcmatch.expression) tumor_types() (in module mhcmatch.expression) U Unit (class in mhcmatch.vector) unit (mhcmatch.vector.Feature attribute) unit() (in module mhcmatch.vector) units (mhcmatch.portfolio.Composition attribute) (mhcmatch.vector.Cassette attribute) (mhcmatch.vector.Selection attribute) units_from_context() (in module mhcmatch.vector) V var (mhcmatch.predict.Prediction attribute) variant_product() (in module mhcmatch.predict) variant_type (mhcmatch.rank.Ranked attribute) vendored_models() (in module mhcmatch.diffusion) viral_r() (in module mhcmatch.luksza) visibility() (in module mhcmatch.portfolio) VISIBILITY_COLUMNS (in module mhcmatch.portfolio) vote (mhcmatch.store.Restriction attribute) W weight_coverage (mhcmatch.cassette.Cassette attribute) weight_escape (mhcmatch.cassette.Cassette attribute) wildtype() (mhcmatch.proteome.Proteome method) wildtypes() (mhcmatch.proteome.Proteome method) window_array() (mhcmatch.proteome.Proteome method) window_genes() (mhcmatch.proteome.Proteome method) windows() (mhcmatch.proteome.Proteome method) worst_junction (mhcmatch.vector.Cassette property) write_map() (in module mhcmatch.vector) write_native() (in module mhcmatch.predict) write_scored_csv() (in module mhcmatch.predict) write_table() (in module mhcmatch.mimics) wt_absent (mhcmatch.rank.Ranked attribute) wt_affinity_nm (mhcmatch.predict.Prediction attribute) WT_COLUMNS (in module mhcmatch.rank) wt_peptide (mhcmatch.predict.Prediction attribute) (mhcmatch.rank.Ranked attribute) Y y_to_ic50() (in module mhcmatch.affinity) yield_ (mhcmatch.cassette.Cassette property) Z ZONES (in module mhcmatch.complement)