Index A | B | C | D | E | F | I | K | L | M | N | O | P | R | S | T | V | W | Y 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) agretopicity (mhcmatch.predict.Prediction attribute) allele (mhcmatch.mimics.MimicResult attribute) (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Restriction attribute) alleles() (mhcmatch.store.Store method) 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_score (mhcmatch.store.Restriction attribute) anchor_terms() (mhcmatch.diffusion.AnchorModel method) AnchorModel (class in mhcmatch.diffusion) anchors (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Decomposition attribute) ASSAY_FLANK (in module mhcmatch.ligand) B background (mhcmatch.ligand.SpanModel attribute) band (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Restriction attribute) band() (in module mhcmatch.calibrate) best_register() (mhcmatch.diffusion.AnchorModel method) best_span() (mhcmatch.ligand.SpanModel method) binder (mhcmatch.mimics.MimicResult attribute) (mhcmatch.store.Restriction attribute) binder_band (mhcmatch.predict.Prediction attribute) binder_rank (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) binder_score() (in module mhcmatch.predict) (mhcmatch.store.Store method) BinderScore (class in mhcmatch.predict) BLOSUM62_BG (in module mhcmatch.pseudoseq) blosum62_conditional() (in module mhcmatch.pseudoseq) build_scorer() (in module mhcmatch.predict) C category (mhcmatch.mimics.MimicResult attribute) class2_from_name() (in module mhcmatch.pseudoseq) class2_key() (in module mhcmatch.pseudoseq) clipped (mhcmatch.ligand.Span attribute) cls (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) cluster() (mhcmatch.pseudoseq.Pseudoseq method) context_score() (mhcmatch.ligand.SpanModel method) core (mhcmatch.ligand.Span attribute) core_start (mhcmatch.ligand.Span attribute) corpus_stats() (in module mhcmatch.calibrate) ctx (mhcmatch.ligand.SpanModel attribute) CTX_KEYS (in module mhcmatch.ligand) D dai (mhcmatch.predict.Prediction attribute) 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_REFS (in module mhcmatch.mimics) E e_value (mhcmatch.mimics.MimicResult attribute) end (mhcmatch.ligand.Span attribute) enrichment (mhcmatch.store.Restriction attribute) F features() (mhcmatch.affinity.AffinityModel method) fetch_pmhc() (in module mhcmatch.store) fetch_proteome() (in module mhcmatch.store) find_source() (mhcmatch.proteome.Proteome method) fit() (mhcmatch.affinity.AffinityModel method) fit_ridge() (in module mhcmatch.affinity) fixed_span() (in module mhcmatch.ligand) FLANK_KEYS (in module mhcmatch.ligand) flanks (mhcmatch.ligand.Span property) 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) I ic50_to_y() (in module mhcmatch.affinity) infer_class() (in module mhcmatch.store) is_binder() (mhcmatch.store.Store method) is_presented() (mhcmatch.store.Store method) K kernel() (mhcmatch.pseudoseq.Pseudoseq method) KMER_LENS (in module mhcmatch.predict) L learn_anchor_weights() (in module mhcmatch.pseudoseq) length_logodds() (mhcmatch.diffusion.AnchorModel method) length_preferences() (mhcmatch.store.Store method) lens (mhcmatch.ligand.SpanModel attribute) LIGAND_KEYS (in module mhcmatch.ligand) load() (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_span_model() (in module mhcmatch.ligand) load_vendored_anchor_model() (in module mhcmatch.diffusion) M Match (class in mhcmatch.search) mhc1_positions() (in module mhcmatch.store) mhcmatch.affinity module mhcmatch.calibrate module mhcmatch.diffusion module mhcmatch.ligand module mhcmatch.logo module mhcmatch.mimics module mhcmatch.predict module mhcmatch.proteome module mhcmatch.pseudoseq module mhcmatch.search module mhcmatch.store module mhcmatch.structure module MimicResult (class in mhcmatch.mimics) mj_energies() (mhcmatch.structure.StructureScorer method) mj_energy() (mhcmatch.structure.StructureScorer method) model_peptide (mhcmatch.predict.Prediction attribute) module mhcmatch.affinity mhcmatch.calibrate mhcmatch.diffusion mhcmatch.ligand mhcmatch.logo mhcmatch.mimics mhcmatch.predict mhcmatch.proteome mhcmatch.pseudoseq mhcmatch.search mhcmatch.store mhcmatch.structure motif() (in module mhcmatch.logo) mutations (mhcmatch.proteome.SourceHit attribute) mutual_information() (in module mhcmatch.pseudoseq) N n_alternatives (mhcmatch.ligand.Span attribute) 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_votes (mhcmatch.store.Restriction attribute) neighbors() (mhcmatch.pseudoseq.Pseudoseq method) normalize_allele() (in module mhcmatch.pseudoseq) O observed_spans() (in module mhcmatch.ligand) offset (mhcmatch.predict.Prediction attribute) P p_present (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Restriction attribute) p_present() (mhcmatch.calibrate.RankCalibrator method) PAD (in module mhcmatch.ligand) padbg (mhcmatch.ligand.SpanModel attribute) panel_sha() (in module mhcmatch.diffusion) parse_fasta() (in module mhcmatch.predict) parse_variant_header() (in module mhcmatch.predict) patient_summary() (in module mhcmatch.mimics) peptide (mhcmatch.ligand.Span attribute) (mhcmatch.predict.BinderScore attribute) (mhcmatch.predict.Prediction attribute) (mhcmatch.search.Match attribute) (mhcmatch.store.Decomposition attribute) percent_rank (mhcmatch.predict.Prediction attribute) percent_rank() (mhcmatch.calibrate.RankCalibrator method) position (mhcmatch.proteome.SourceHit attribute) 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) Prediction (class in mhcmatch.predict) presentation (mhcmatch.store.Decomposition attribute) presentation_rank (mhcmatch.predict.BinderScore attribute) presented_span() (in module mhcmatch.ligand) processing_score() (in module mhcmatch.ligand) protein (mhcmatch.proteome.SourceHit attribute) Proteome (class in mhcmatch.proteome) Pseudoseq (class in mhcmatch.pseudoseq) R random_peptides() (in module mhcmatch.calibrate) rank (mhcmatch.store.Restriction attribute) RankCalibrator (class in mhcmatch.calibrate) read_fasta() (in module mhcmatch.proteome) ref_peptide (mhcmatch.proteome.SourceHit attribute) render() (in module mhcmatch.logo) resolve_allele() (in module mhcmatch.pseudoseq) resolve_anchor_index() (in module mhcmatch.store) Restriction (class in mhcmatch.store) restriction() (mhcmatch.store.Store method) S save_vendored_anchor_model() (in module mhcmatch.diffusion) scan() (in module mhcmatch.mimics) scan_protein() (mhcmatch.store.Store method) score (mhcmatch.ligand.Span attribute) (mhcmatch.search.Match attribute) score() (mhcmatch.diffusion.AnchorModel method) SCORED_COLUMNS (in module mhcmatch.predict) search() (in module mhcmatch.search) shared_kmers (mhcmatch.search.Match attribute) shrink() (mhcmatch.pseudoseq.Pseudoseq method) significant (mhcmatch.mimics.MimicResult attribute) source (mhcmatch.ligand.Span attribute) (mhcmatch.predict.Prediction attribute) SourceHit (class in mhcmatch.proteome) Span (class in mhcmatch.ligand) SpanModel (class in mhcmatch.ligand) start (mhcmatch.ligand.Span attribute) Store (class in mhcmatch.store) STRUCTURE_FLANK (in module mhcmatch.ligand) StructureScorer (class in mhcmatch.structure) support (mhcmatch.ligand.Span attribute) synth_peptide (mhcmatch.predict.Prediction attribute) T tcr_facing (mhcmatch.predict.Prediction attribute) (mhcmatch.store.Decomposition attribute) template_for() (mhcmatch.structure.StructureScorer method) tile() (in module mhcmatch.predict) top_mimic (mhcmatch.mimics.MimicResult attribute) top_subs (mhcmatch.mimics.MimicResult attribute) V var (mhcmatch.predict.Prediction attribute) vote (mhcmatch.store.Restriction attribute) W wildtype() (mhcmatch.proteome.Proteome method) write_native() (in module mhcmatch.predict) write_scored_csv() (in module mhcmatch.predict) write_table() (in module mhcmatch.mimics) wt_affinity_nm (mhcmatch.predict.Prediction attribute) wt_peptide (mhcmatch.predict.Prediction attribute) Y y_to_ic50() (in module mhcmatch.affinity)