Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Y | Z A a (tcren.mechanics.springs.InterfaceSprings attribute) (tcren.stacking.RingPair attribute) AA (in module tcren.potts) aa (tcren.cpl.ResponseMatrix attribute) (tcren.energetics.scoring.RecognitionMatrix attribute) (tcren.structure.model.Residue attribute) AA20 (in module tcren.cpl) (in module tcren.potential.model) AA21 (in module tcren.potential.model) aaindex() (in module tcren.potential.aaindex) AAindexEntry (class in tcren.potential.aaindex) accept_rate (tcren.mechanics.dynamics.Stability attribute) accession (tcren.potential.aaindex.AAindexEntry attribute) af_band() (in module tcren.reliability) ais_log_z() (in module tcren.potts) alanine_scan() (in module tcren.energetics.mutation) align_to_canonical() (in module tcren.docking.pipeline) align_to_native() (in module tcren.docking.align) all_atom_contacts() (in module tcren.contacts.geometry) allele (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) allele_info (tcren.structure.model.Chain attribute) alpha (tcren.potts.PottsModel attribute) (tcren.score.model.Joint attribute) alphabet (tcren.potential.model.Potential attribute) (tcren.potts.PottsModel attribute) alphabeta_ids() (in module tcren.potential.redundancy) anchor_ca_rmsd (tcren.refine.PeptideRMSD attribute) (tcren.refine.rmsd.PeptideRMSD attribute) anchor_indices() (in module tcren.refine.anchors) anchor_rmsd (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) anchors (tcren.refine.anchors.Decomposition attribute) (tcren.refine.Decomposition attribute) (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) angles (tcren.geometry.LoopInternalCoords attribute) annotate() (in module tcren.cli) annotate_batch() (in module tcren.annotation.batch) annotate_chain() (in module tcren.annotation.arda_adapter) annotate_chains() (in module tcren.annotation.arda_adapter) annotate_mhc() (in module tcren.mhc.regions) annotate_mhc_batch() (in module tcren.mhc.regions) annotate_pseudo() (in module tcren.mhc.pseudo) annotate_structure_set() (in module tcren.annotation.batch) annotate_tcr_chains() (in module tcren.annotation.arda_adapter) annotate_tcr_chains_scored() (in module tcren.annotation.arda_adapter) anomaly() (tcren.score.model.Joint method) anomaly_on() (tcren.score.model.Joint method) apex_x (tcren.contactmap.ModeCentroid attribute) apply_mhc_calls() (in module tcren.mhc.mapper) apply_records() (in module tcren.annotation.arda_adapter) apply_transform() (in module tcren.docking.align) artefact_directions() (in module tcren.reliability) as_matrix() (tcren.potential.model.Potential method) assess() (in module tcren.cli) Atom (class in tcren.structure.model) atoms (tcren.structure.model.Residue attribute) authors (tcren.potential.aaindex.AAindexEntry attribute) available() (tcren.refine.engines.base.Engine method) (tcren.refine.engines.ccd.CcdEngine method) (tcren.refine.engines.dope.DopeEngine method) (tcren.refine.engines.openmm_engine.OpenMMEngine method) (tcren.refine.engines.promod3_engine.ProMod3Engine method) (tcren.score.ScoreModel method) available_bands() (in module tcren.reliability) available_pairs() (in module tcren.potts) Axis (class in tcren.viz.pymol) axis (tcren.mechanics.springs.InterfaceSprings attribute) B b (tcren.mechanics.springs.InterfaceSprings attribute) (tcren.stacking.RingPair attribute) BACKBONE_ATOMS (in module tcren.contacts.geometry) backbone_rmsd (tcren.refine.PeptideRMSD attribute) (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) (tcren.refine.rmsd.PeptideRMSD attribute) backbone_torsions() (in module tcren.mechanics.dynamics) background_peptides() (in module tcren.scoring_rank) balanced_weights() (in module tcren.potential.redundancy) BANNED (in module tcren.score.transform) best_ref (tcren.mhc.linker.MhcAlignmentCheck attribute) beta_matrix (tcren.potts.PottsModel attribute) betancourt() (in module tcren.potential.model) binder_score() (in module tcren.score) (tcren.score.ScoreModel method) binding_mode() (in module tcren.contactmap) bits (tcren.mhc.mapper.MhcCall attribute) BOND_CA (in module tcren.geometry) BONDI_RADII (in module tcren.clashes) bonds (tcren.geometry.LoopInternalCoords attribute) bootstrap() (in module tcren.paper.bootstrap) bound_unbound() (in module tcren.potts) bucket_edges() (in module tcren.potts) build() (in module tcren.mhc.reference) build_canonical_frame() (in module tcren.docking.frame) build_mhc_ref() (in module tcren.cli) bundled() (tcren.potts.PottsModel class method) by_partner (tcren.clashes.ClashReport attribute) by_seq_index() (tcren.structure.model.Chain method) by_type() (tcren.structure.model.Structure method) C c0 (tcren.potential.model.HydrophobicityFit attribute) c1 (tcren.potential.model.HydrophobicityFit attribute) c2 (tcren.potential.model.HydrophobicityFit attribute) c_term_extra (tcren.mhc.linker.MhcAlignmentCheck attribute) ca (tcren.structure.model.Residue property) ca_contacts_table() (in module tcren.project2d.tables) ca_distance_matrix() (in module tcren.contacts.geometry) ca_rmsd (tcren.refine.PeptideRMSD attribute) (tcren.refine.rmsd.PeptideRMSD attribute) calls_from_hits() (in module tcren.mhc.mapper) CANONICAL_AXES (in module tcren.viz.pymol) canonical_frame() (in module tcren.docking.frame) canonical_groove() (in module tcren.mhc.domains) canonicalize_structure() (in module tcren.docking.pipeline) CanonResult (class in tcren.docking.frame) catalogue() (in module tcren.potential.aaindex) cb (tcren.structure.model.Residue property) cb_or_ca (tcren.structure.model.Residue property) CcdEngine (class in tcren.refine.engines.ccd) cdr3_internal_coords() (in module tcren.geometry) cdr3_torsions() (in module tcren.torsions) CDR_LOOPS (in module tcren.potts) cell_counts() (in module tcren.topology.footprint) CELL_LOOPS (in module tcren.topology.footprint) cell_type (tcren.annotation.cgene.ConstantCall attribute) (tcren.docking.angles.DockingAngles attribute) (tcren.structure.model.Structure attribute) cell_type() (in module tcren.annotation.cgene) central_strain() (in module tcren.energetics.scoring) centred_potential() (in module tcren.potts) centroid (tcren.stacking.Ring attribute) centroid_distance (tcren.stacking.RingPair attribute) Chain (class in tcren.structure.model) chain() (tcren.structure.model.Structure method) chain_class (tcren.annotation.cgene.ConstantCall attribute) CHAIN_COLOURS (in module tcren.viz.pymol) chain_id (tcren.annotation.cgene.ConstantCall attribute) (tcren.mhc.linker.MhcAlignmentCheck attribute) (tcren.mhc.mapper.MhcCall attribute) (tcren.stacking.Ring attribute) (tcren.structure.model.Chain attribute) chain_map (tcren.docking.frame.CanonResult attribute) chain_role (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) chain_supertype (tcren.structure.model.Chain attribute) chain_torsions() (in module tcren.torsions) chain_type (tcren.structure.model.Chain attribute) chains (tcren.structure.model.Structure attribute) channel_scores() (in module tcren.score) (tcren.score.ScoreModel method) channels (tcren.topology.surface.SurfaceMap attribute) check() (in module tcren.provenance) check_against_mhc() (in module tcren.mhc.linker) check_oriented_complex() (in module tcren.docking.pipeline) check_register() (in module tcren.refine) (in module tcren.refine.register) chi_axes() (in module tcren.energetics.rotamers) cif_lines() (in module tcren.structure.io) cigar (tcren.mhc.mapper.MhcCall attribute) clash_score (tcren.clashes.ClashReport attribute) clashes (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) clashing (tcren.clashes.ClashReport property) ClashPair (class in tcren.clashes) ClashReport (class in tcren.clashes) CLASSES (in module tcren.potts) classes (tcren.potts.PottsModel attribute) classify_chain_constant() (in module tcren.annotation.cgene) classify_chains() (in module tcren.annotation.chains) classify_constants() (in module tcren.annotation.cgene) classify_contact() (in module tcren.project2d.tables) classify_contacts() (in module tcren.contact_types) CLIP (tcren.score.transform.Transformer attribute) cluster_se() (in module tcren.potts) cluster_weights() (in module tcren.potential.redundancy) color_for() (in module tcren.viz.palette) colour() (in module tcren.potts) cols (tcren.potential.aaindex.AAindexEntry attribute) column_of() (tcren.cpl.ResponseMatrix method) compare() (in module tcren.paper.helpers) compare_potentials() (in module tcren.analysis) COMPARE_WINDOW (in module tcren.topology.surface) complex_species (tcren.structure.model.Structure attribute) components() (tcren.potential.model.Potential method) composite() (in module tcren.viz.pymol) conf_mu (tcren.score.ScoreModel attribute) confidence_residual() (in module tcren.score) (tcren.score.ScoreModel method) connected_correlations() (in module tcren.potts) constant_span() (in module tcren.annotation.cgene) ConstantCall (class in tcren.annotation.cgene) contact_map() (in module tcren.potts) contact_order() (in module tcren.topology.literature) contact_probabilities() (in module tcren.energetics.rotamers) (in module tcren.potts) contact_stability() (in module tcren.mechanics.stability) contact_table() (in module tcren.paper.helpers) contact_type_counts() (in module tcren.contact_types) ContactDefinition (class in tcren.contacts.definitions) ContactMap (class in tcren.contactmap) contacts (tcren.contactmap.ContactMap attribute) (tcren.pipeline.PipelineResult attribute) contacts() (in module tcren.cli) contacts_per_structure() (in module tcren.analysis) contacts_table() (in module tcren.project2d.tables) coord (tcren.structure.model.Atom attribute) coordinates() (tcren.score.ScoreModel method) coords3d (tcren.project2d.frame.ProjectionResult attribute) copy_external_inputs() (in module tcren.paper.bootstrap) copy_legacy_results() (in module tcren.paper.bootstrap) CORNERS (in module tcren.viz.pymol) count_free_energy() (in module tcren.potts) count_profile() (in module tcren.potts) coupling (tcren.potts.PottsModel attribute) coupling() (in module tcren.cohort) coupling_array() (tcren.potts.PottsModel method) coupling_matrix() (in module tcren.potts) coupling_matrix_name (tcren.potts.PottsModel attribute) coupling_residues() (in module tcren.mechanics.springs) cov (tcren.score.model.Joint attribute) cpl_cmd() (in module tcren.cli) CROSS_DJ (in module tcren.potts) crossing_angle (tcren.docking.angles.DockingAngles attribute) crossing_angle_signed (tcren.docking.angles.DockingAngles attribute) crossing_incident_from_vector() (in module tcren.docking.angles) cutoff (tcren.potts.PottsModel attribute) D d (tcren.docking.tcrdock_geometry.DockingGeometry attribute) d1 (tcren.contacts.definitions.ContactDefinition attribute) d2 (tcren.contacts.definitions.ContactDefinition attribute) d3 (tcren.contacts.definitions.ContactDefinition attribute) data_dir() (in module tcren.paths) DBIN (in module tcren.potts) dbin (tcren.potts.PottsModel attribute) ddg() (in module tcren.energetics.mutation) ddg_cmd() (in module tcren.cli) decompose() (in module tcren.refine.anchors) (tcren.potential.model.Potential method) Decomposition (class in tcren.refine) (class in tcren.refine.anchors) DEFAULT_ANCHOR_W (in module tcren.mechanics.dynamics) DEFAULT_EXTENT (in module tcren.topology.surface) DEFAULT_RIDGE (in module tcren.potts) DEFAULT_SIGMA (in module tcren.mechanics.dynamics) DEFAULT_STEP (in module tcren.energetics.rotamers) DEFAULT_TEMPERATURE (in module tcren.energetics.rotamers) (in module tcren.mechanics.dynamics) definition (tcren.viz.pymol.Axis attribute) delta_f_empty() (in module tcren.potts) delta_f_threshold() (in module tcren.potts) derive_potential() (in module tcren.cli) derive_tcren() (in module tcren.potential.derive) derive_tcren_by_type() (in module tcren.potential.derive) derive_tcren_loo() (in module tcren.potential.derive) description (tcren.potential.aaindex.AAindexEntry attribute) DESCRIPTORS (in module tcren.descriptors.catalogue) descriptors() (in module tcren.descriptors.catalogue) design() (in module tcren.potts) DETAIL (in module tcren.descriptors.catalogue) detect_linked_peptide() (in module tcren.mhc.linker) detect_reverse_dock() (in module tcren.docking.exceptions) DETERMINED (in module tcren.score.transform) dihedral() (in module tcren.torsions) discover_similar() (in module tcren.recent) docking_angles() (in module tcren.docking.angles) docking_geometry() (in module tcren.docking.tcrdock_geometry) DockingAngles (class in tcren.docking.angles) DockingGeometry (class in tcren.docking.tcrdock_geometry) DopeEngine (class in tcren.refine.engines.dope) download_human() (in module tcren.mhc.imgt) download_mouse() (in module tcren.mhc.imgt) drift (tcren.mechanics.dynamics.Stability attribute) E edges() (in module tcren.potts) eigenvalue_share (tcren.potential.model.HydrophobicityFit attribute) element (tcren.structure.model.Atom attribute) end_seq_index (tcren.structure.model.RegionMarkup attribute) energy (tcren.energetics.scoring.RecognitionMatrix attribute) (tcren.mechanics.dynamics.Stability attribute) (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) energy() (in module tcren.cli) (in module tcren.potts) (tcren.potential.model.PotentialDecomposition method) energy_gap (tcren.mechanics.dynamics.Stability attribute) energy_start (tcren.mechanics.dynamics.Stability attribute) Engine (class in tcren.refine.engines.base) engine (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) EngineUnavailable entry() (in module tcren.potential.aaindex) epitope_weights() (in module tcren.potential.redundancy) (in module tcren.score.fit) equimolar_effect() (in module tcren.cpl) eta() (in module tcren.potts) exact_log_z() (in module tcren.potts) exp_lost (tcren.mechanics.stability.StabilityReport attribute) explain() (in module tcren.cli) extent (tcren.topology.surface.SurfaceMap attribute) extra (tcren.pipeline.PipelineResult attribute) F factorised_log_z() (in module tcren.potts) features() (in module tcren.cli) fetch_data() (in module tcren.cli) fetch_hf_structures() (in module tcren.paper.bootstrap) fetch_ids() (in module tcren.recent) fetch_pdb_dates() (in module tcren.paper.bootstrap) fetch_recent() (in module tcren.cli) fetch_vdjdb() (in module tcren.paper.bootstrap) find_metadata() (in module tcren.metadata) fit() (tcren.score.model.Joint method) (tcren.score.transform.Transformer method) fit_holdout() (in module tcren.score.fit) fit_holdout_cmd() (in module tcren.cli) fit_potts() (in module tcren.potts) fix_register() (in module tcren.refine) (in module tcren.refine.register) flexpep_available() (in module tcren.refine.oracle_flexpep) flexpep_refine() (in module tcren.refine.oracle_flexpep) footprint() (in module tcren.cli) footprint_batch() (in module tcren.topology.footprint) FOOTPRINT_FEATURES (in module tcren.topology.footprint) footprint_features() (in module tcren.topology.footprint) FOOTPRINT_SIZE_FEATURES (in module tcren.topology.footprint) footprint_topology_features() (in module tcren.topology.footprint) footprint_width_alpha (tcren.contactmap.ModeCentroid attribute) footprint_width_beta (tcren.contactmap.ModeCentroid attribute) frac_marg_lt1 (tcren.mechanics.stability.StabilityReport attribute) frac_robust (tcren.mechanics.stability.StabilityReport attribute) frame (tcren.docking.frame.CanonResult attribute) (tcren.project2d.frame.ProjectionResult attribute) from_csv() (tcren.potential.model.Potential class method) from_json() (tcren.potts.PottsModel class method) from_structure() (tcren.contactmap.ContactMap class method) FULL_FEATURES (in module tcren.descriptors.catalogue) G g_class (tcren.potts.PottsModel attribute) g_dist (tcren.potts.PottsModel attribute) g_region (tcren.potts.PottsModel attribute) g_role (tcren.potts.PottsModel attribute) gauge() (in module tcren.potts) gene (tcren.annotation.cgene.ConstantCall attribute) gibbs() (in module tcren.potts) gizmo_cgo() (in module tcren.viz.pymol) gizmo_scene() (in module tcren.viz.pymol) graft_tcr() (in module tcren.shuffle) graph_features() (in module tcren.topology.graph) grid (tcren.topology.surface.SurfaceMap attribute) groove_for() (in module tcren.mhc.domains) groove_importance_scene() (in module tcren.viz.pymol) GROOVE_REGIONS (in module tcren.potts) groove_rmsd (tcren.refine.PeptideRMSD attribute) (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) (tcren.refine.rmsd.PeptideRMSD attribute) groove_scene() (in module tcren.viz.pymol) H h() (tcren.potential.model.PotentialDecomposition method) h_par (tcren.potts.PottsModel attribute) h_rec (tcren.potts.PottsModel attribute) has_clashes() (in module tcren.clashes) height (tcren.docking.angles.TcrPlacement attribute) (tcren.project2d.frame.ProjectionResult property) holdout_manifest() (in module tcren.score) holdout_model() (in module tcren.score) hydrophobicity_fit() (tcren.potential.model.Potential method) HydrophobicityFit (class in tcren.potential.model) I identify() (in module tcren.potential.aaindex) identity (tcren.mhc.mapper.MhcCall attribute) import_structure() (in module tcren.structure.io) importance_scene() (in module tcren.viz.pymol) incident_angle (tcren.docking.angles.DockingAngles attribute) index (tcren.potential.model.HydrophobicityFit attribute) (tcren.potential.model.PotentialDecomposition attribute) infer_class() (in module tcren.refine.anchors) info (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) info() (in module tcren.cli) insertion_code (tcren.structure.model.Residue attribute) interface (tcren.energetics.scoring.RecognitionMatrix attribute) interface() (tcren.contactmap.ContactMap method) interface_clashes() (in module tcren.clashes) interface_class (tcren.cpl.ResponseMatrix attribute) interface_energy() (in module tcren.refine) (in module tcren.refine.interface) interface_mechanics() (in module tcren.mechanics.springs) interface_scene() (in module tcren.viz.pymol) interface_springs() (in module tcren.mechanics.springs) INTERFACE_SYMMETRY_FEATURES (in module tcren.descriptors.catalogue) INTERFACES (in module tcren.cpl) InterfaceSprings (class in tcren.mechanics.springs) interplanar_angle (tcren.stacking.RingPair attribute) intra_peptide_energy() (in module tcren.energetics.scoring) intra_weight (tcren.mechanics.dynamics.Stability attribute) INVARIANCE (in module tcren.descriptors.catalogue) INVARIANCE_CLASSES (in module tcren.descriptors.catalogue) inversion_flag() (in module tcren.reliability) irls() (in module tcren.potts) is_mhc (tcren.mhc.linker.MhcAlignmentCheck property) is_real_interface() (in module tcren.binder) (in module tcren.binder.noise) is_structure_file() (in module tcren.structure.io) iter_annotated_set() (in module tcren.annotation.batch) iter_structures() (in module tcren.structure.io) iter_typed() (in module tcren.annotation.batch) iterations (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) J j() (tcren.potential.model.PotentialDecomposition method) join_metadata() (in module tcren.metadata) Joint (class in tcren.score.model) joint (tcren.potts.PottsModel attribute) journal (tcren.potential.aaindex.AAindexEntry attribute) K k (tcren.mechanics.springs.InterfaceSprings attribute) kernel (tcren.potts.PottsModel attribute) kernel_names() (in module tcren.potts) kernel_se (tcren.potts.PottsModel attribute) kernel_table() (in module tcren.potts) keskin() (in module tcren.potential.model) keys (tcren.project2d.frame.ProjectionResult attribute) kind (tcren.potential.aaindex.AAindexEntry attribute) kind() (in module tcren.score.transform) L label (tcren.viz.pymol.Axis attribute) label_points() (in module tcren.viz.pymol) lam (tcren.score.transform.Transformer attribute) lam1 (tcren.score.model.Joint attribute) lateral (tcren.stacking.RingPair attribute) letter (tcren.viz.pymol.Axis attribute) LITERATURE_FEATURES (in module tcren.topology.literature) literature_features() (in module tcren.topology.literature) load_interface_contacts() (in module tcren.analysis) loc (tcren.score.transform.Transformer attribute) locus (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) log_odds() (tcren.score.model.Joint method) LoopInternalCoords (class in tcren.geometry) M main() (in module tcren.cli) make_decoys() (in module tcren.shuffle) map_mhc() (in module tcren.mhc.mapper) markup (tcren.pipeline.PipelineResult attribute) matrix (tcren.potential.aaindex.AAindexEntry attribute) (tcren.potential.model.Potential attribute) MATRIX_FEATURES (in module tcren.topology.graph) matrix_features() (in module tcren.topology.graph) MAX_GAP (in module tcren.topology.surface) max_overlap (tcren.clashes.ClashReport attribute) mean (tcren.potential.model.PotentialDecomposition attribute) mean_bfactor() (in module tcren.structure.io) mean_margin (tcren.mechanics.stability.StabilityReport attribute) mechanics() (in module tcren.cli) mhc_annotation() (in module tcren.annotation.batch) mhc_calls (tcren.pipeline.PipelineResult attribute) (tcren.structure.model.Structure attribute) mhc_class (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) (tcren.refine.anchors.Decomposition attribute) (tcren.refine.Decomposition attribute) mhc_class() (in module tcren.shuffle) MHC_HELIX_REGIONS (in module tcren.topology.graph) MHC_PARTNER (in module tcren.potts) mhc_unit_y (tcren.docking.tcrdock_geometry.DockingGeometry attribute) mhc_unit_z (tcren.docking.tcrdock_geometry.DockingGeometry attribute) MhcAlignmentCheck (class in tcren.mhc.linker) MhcAllele (class in tcren.mhc.imgt) MhcCall (class in tcren.mhc.mapper) MIN_CONSTANT_SCORE (in module tcren.annotation.cgene) MIN_COORDINATES (tcren.score.ScoreModel attribute) mj() (in module tcren.potential.model) mj1996() (in module tcren.potential.model) mj_partition_energy() (in module tcren.potential.model) ModeCentroid (class in tcren.contactmap) model_peptide() (in module tcren.refine.model) ModelResult (class in tcren.refine.engines.base) (class in tcren.refine.model) module tcren.analysis tcren.annotation.arda_adapter tcren.annotation.batch tcren.annotation.cgene tcren.annotation.chains tcren.binder tcren.binder.noise tcren.clashes tcren.cli tcren.cohort tcren.contact_types tcren.contactmap tcren.contacts.definitions tcren.contacts.geometry tcren.contacts.table tcren.cpl tcren.descriptors tcren.descriptors.catalogue tcren.descriptors.compute tcren.descriptors.table tcren.docking.align tcren.docking.angles tcren.docking.chains tcren.docking.exceptions tcren.docking.frame tcren.docking.graft tcren.docking.pipeline tcren.docking.superimpose tcren.docking.tcrdock_geometry tcren.energetics tcren.energetics.mutation tcren.energetics.rotamers tcren.energetics.scoring tcren.geometry tcren.mechanics tcren.mechanics.dynamics tcren.mechanics.springs tcren.mechanics.stability tcren.metadata tcren.mhc.domains tcren.mhc.imgt tcren.mhc.linker tcren.mhc.mapper tcren.mhc.pseudo tcren.mhc.reference tcren.mhc.regions tcren.oracle tcren.paper.bootstrap tcren.paper.helpers tcren.paths tcren.pipeline tcren.potential.aaindex tcren.potential.derive tcren.potential.model tcren.potential.redundancy tcren.potts tcren.project2d.frame tcren.project2d.pockets tcren.project2d.tables tcren.provenance tcren.recent tcren.recognition tcren.refine tcren.refine.anchors tcren.refine.engines.base tcren.refine.engines.ccd tcren.refine.engines.dope tcren.refine.engines.openmm_engine tcren.refine.engines.promod3_engine tcren.refine.interface tcren.refine.model tcren.refine.oracle_flexpep tcren.refine.register tcren.refine.rmsd tcren.refine.substitute tcren.score.fit tcren.score.model tcren.score.transform tcren.scoring_rank tcren.shuffle tcren.stacking tcren.structure.io tcren.structure.model tcren.topology tcren.topology.footprint tcren.topology.graph tcren.topology.literature tcren.topology.pose tcren.topology.surface tcren.torsions tcren.viz.palette tcren.viz.pocket3d tcren.viz.pymol tcren.viz.surface2d tcren.viz.svg2d moments() (in module tcren.reliability) mu (tcren.score.model.Joint attribute) mu_star() (in module tcren.potts) multi_contacts() (in module tcren.contacts.definitions) mutation_effect() (in module tcren.cpl) N n_anchor_atoms (tcren.docking.align.OrientationResult attribute) (tcren.docking.frame.CanonResult attribute) n_atoms (tcren.topology.surface.SurfaceMap attribute) n_backbone (tcren.refine.PeptideRMSD attribute) (tcren.refine.rmsd.PeptideRMSD attribute) n_ca (tcren.geometry.LoopInternalCoords attribute) (tcren.refine.PeptideRMSD attribute) (tcren.refine.rmsd.PeptideRMSD attribute) n_cdr (tcren.docking.angles.TcrPlacement attribute) N_CHI (in module tcren.energetics.rotamers) n_clashes (tcren.clashes.ClashReport attribute) n_contacts (tcren.mechanics.stability.StabilityReport attribute) (tcren.potts.PottsModel attribute) n_contacts_alpha (tcren.contactmap.ModeCentroid attribute) n_contacts_beta (tcren.contactmap.ModeCentroid attribute) n_missing (tcren.potential.aaindex.AAindexEntry property) n_parameters() (tcren.potts.PottsModel method) n_peptide_atoms (tcren.clashes.ClashReport attribute) n_samples (tcren.mechanics.dynamics.Stability attribute) n_severe (tcren.clashes.ClashReport attribute) n_sites (tcren.potts.PottsModel attribute) n_structures (tcren.potts.PottsModel attribute) n_term_extra (tcren.mhc.linker.MhcAlignmentCheck attribute) n_va (tcren.docking.angles.DockingAngles attribute) n_vb (tcren.docking.angles.DockingAngles attribute) name (tcren.potential.model.HydrophobicityFit attribute) (tcren.potential.model.Potential attribute) (tcren.potential.model.PotentialDecomposition attribute) (tcren.refine.engines.base.Engine attribute) (tcren.refine.engines.ccd.CcdEngine attribute) (tcren.refine.engines.dope.DopeEngine attribute) (tcren.refine.engines.openmm_engine.OpenMMEngine attribute) (tcren.refine.engines.promod3_engine.ProMod3Engine attribute) (tcren.structure.model.Atom attribute) names (tcren.score.model.Joint attribute) (tcren.score.transform.Transformer attribute) native2026_ids() (in module tcren.recent) native_dir() (in module tcren.paths) native_peptide() (in module tcren.refine) (in module tcren.refine.anchors) native_reference() (in module tcren.cohort) neck (tcren.geometry.LoopInternalCoords attribute) neighbour_counts() (in module tcren.potts) neoantigen_ddg() (in module tcren.energetics.mutation) NON_ENERGY (in module tcren.potential.aaindex) nonredundant_ids() (in module tcren.potential.redundancy) normal (tcren.stacking.Ring attribute) notes (tcren.potts.PottsModel attribute) O occupancy() (tcren.topology.surface.SurfaceMap method) offset (tcren.docking.angles.TcrPlacement attribute) offset() (tcren.potential.model.Potential method) OFFSETS (in module tcren.potts) one_body (tcren.potential.model.PotentialDecomposition attribute) one_body() (tcren.potential.model.HydrophobicityFit method) OpenMMEngine (class in tcren.refine.engines.openmm_engine) OPERATOR (in module tcren.descriptors.catalogue) OPERATOR_OBJECT (in module tcren.descriptors.catalogue) orient() (in module tcren.cli) OrientationResult (class in tcren.docking.align) oriented (tcren.pipeline.PipelineResult attribute) out_names() (tcren.score.transform.Transformer method) overlap (tcren.clashes.ClashPair attribute) overlay_scene() (in module tcren.viz.pymol) P pair (tcren.potential.model.PotentialDecomposition attribute) PALETTES (in module tcren.viz.pymol) paper_bootstrap() (in module tcren.cli) parse_aaindex3() (in module tcren.potential.aaindex) parse_header() (in module tcren.mhc.reference) parse_human() (in module tcren.mhc.imgt) parse_mouse() (in module tcren.mhc.imgt) parse_structure() (in module tcren.structure.io) participation_coefficient() (in module tcren.topology.literature) partition_chain() (in module tcren.mhc.regions) partition_mhc() (in module tcren.mhc.regions) partner_chain_type (tcren.clashes.ClashPair attribute) partner_residue (tcren.clashes.ClashPair attribute) pdb_id (tcren.contactmap.ContactMap attribute) (tcren.pipeline.PipelineResult attribute) (tcren.structure.model.Structure attribute) pdb_index (tcren.structure.model.Residue attribute) pdb_lines() (in module tcren.structure.io) peptide (tcren.cpl.ResponseMatrix attribute) (tcren.mechanics.dynamics.Stability attribute) (tcren.refine.anchors.Decomposition attribute) (tcren.refine.Decomposition attribute) (tcren.topology.surface.SurfaceMap attribute) peptide_free_energy() (in module tcren.potts) peptide_internal (tcren.contactmap.ContactMap attribute) peptide_internal_contacts() (in module tcren.contacts.geometry) PEPTIDE_INTERNAL_FEATURES (in module tcren.descriptors.catalogue) peptide_length (tcren.contactmap.ContactMap attribute) peptide_positions() (in module tcren.energetics.scoring) peptide_residue (tcren.clashes.ClashPair attribute) peptide_rmsd() (in module tcren.refine) (in module tcren.refine.rmsd) peptide_score() (in module tcren.score) peptide_stability() (in module tcren.mechanics.dynamics) PeptideRMSD (class in tcren.refine) (class in tcren.refine.rmsd) percentile_rank() (in module tcren.scoring_rank) phi (tcren.cpl.ResponseMatrix attribute) phi_mhc (tcren.cpl.ResponseMatrix attribute) phi_score() (in module tcren.cohort) phi_tcr (tcren.cpl.ResponseMatrix attribute) PHI_TERMS (in module tcren.cohort) PI_FROZEN (in module tcren.reliability) pipeline() (in module tcren.cli) PipelineResult (class in tcren.pipeline) pmid (tcren.potential.aaindex.AAindexEntry attribute) pocket_markers() (in module tcren.project2d.pockets) pose_consistency() (in module tcren.topology.pose) POSE_FEATURES (in module tcren.topology.pose) POSE_FEATURES_CONTACT (in module tcren.topology.pose) POSE_FEATURES_DEGREE (in module tcren.topology.pose) POSE_FEATURES_SHELL (in module tcren.topology.pose) pose_score() (in module tcren.score) (tcren.score.ScoreModel method) position_distribution() (in module tcren.analysis) position_profile() (in module tcren.energetics.scoring) position_scan() (in module tcren.cpl) POSITION_SCHEMES (in module tcren.energetics.scoring) position_weights() (in module tcren.energetics.scoring) positions (tcren.cpl.ResponseMatrix attribute) (tcren.energetics.scoring.RecognitionMatrix attribute) Potential (class in tcren.potential.model) potential_long() (in module tcren.analysis) potential_matrix() (in module tcren.analysis) PotentialDecomposition (class in tcren.potential.model) potts_contacts_cmd() (in module tcren.cli) potts_fit_cmd() (in module tcren.cli) potts_map_cmd() (in module tcren.cli) potts_scan_cmd() (in module tcren.cli) potts_score_cmd() (in module tcren.cli) PottsModel (class in tcren.potts) predict() (tcren.score.model.Joint method) predict_anchors() (in module tcren.refine) (in module tcren.refine.anchors) presentation (tcren.refine.anchors.Decomposition attribute) (tcren.refine.Decomposition attribute) prior (tcren.score.model.Joint attribute) probe_rotation() (in module tcren.viz.pymol) project() (tcren.score.model.Joint method) project_structure() (in module tcren.project2d.frame) ProjectionResult (class in tcren.project2d.frame) ProMod3Engine (class in tcren.refine.engines.promod3_engine) PROMOTED_POSE_FEATURES (in module tcren.topology.graph) pseudo_loglik (tcren.potts.PottsModel attribute) pyrosetta_available() (in module tcren.refine.oracle_flexpep) Q q (tcren.potential.model.HydrophobicityFit attribute) q_coupled() (in module tcren.cohort) Q_FEATURES (in module tcren.cohort) Q_FEATURES_CORE (in module tcren.cohort) Q_FEATURES_GEOM (in module tcren.cohort) q_score() (in module tcren.cohort) qend (tcren.mhc.mapper.MhcCall attribute) qstart (tcren.mhc.mapper.MhcCall attribute) query_end (tcren.mhc.linker.MhcAlignmentCheck attribute) query_start (tcren.mhc.linker.MhcAlignmentCheck attribute) R r2 (tcren.potential.model.HydrophobicityFit attribute) radius (tcren.potts.PottsModel attribute) rank() (in module tcren.cli) reach_max() (in module tcren.geometry) reachability_floor() (in module tcren.geometry) read() (in module tcren.provenance) read_metadata() (in module tcren.metadata) reason (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) recent_dir() (in module tcren.recent) receptor_names (tcren.score.ScoreModel attribute) RECOGNITION_FEATURES (in module tcren.descriptors.catalogue) recognition_features() (in module tcren.descriptors.compute) recognition_matrix() (in module tcren.energetics.scoring) recognition_table() (in module tcren.descriptors.table) RecognitionMatrix (class in tcren.energetics.scoring) recognize() (in module tcren.cli) reference_db() (in module tcren.mhc.reference) reference_delta() (in module tcren.energetics.mutation) reference_fasta() (in module tcren.mhc.reference) reference_id (tcren.docking.align.OrientationResult attribute) (tcren.docking.frame.CanonResult attribute) (tcren.project2d.frame.ProjectionResult attribute) reference_structure_path() (in module tcren.paths) referenced() (tcren.cpl.ResponseMatrix method) REFERENCES (in module tcren.cpl) refine() (in module tcren.cli) refine_peptide() (in module tcren.refine) region_contact_counts() (in module tcren.analysis) region_pair_contacts() (in module tcren.project2d.tables) region_pair_summary() (in module tcren.project2d.tables) region_type (tcren.structure.model.RegionMarkup attribute) RegionMarkup (class in tcren.structure.model) REGIONS (in module tcren.potts) regions (tcren.potts.PottsModel attribute) (tcren.structure.model.Chain attribute) registered_map() (in module tcren.contactmap) RegisterReport (class in tcren.refine) (class in tcren.refine.register) registry_digest() (in module tcren.provenance) reliability_reference() (in module tcren.reliability) rename_chains() (in module tcren.docking.chains) render() (in module tcren.viz.pymol) render_complementarity_map() (in module tcren.viz.svg2d) render_surface_map() (in module tcren.viz.surface2d) repack() (in module tcren.energetics.rotamers) representative_atom_contacts() (in module tcren.contacts.geometry) Residue (class in tcren.structure.model) residue_annotation() (in module tcren.contacts.table) residue_deltas() (in module tcren.score) residue_importance() (in module tcren.viz.pymol) residue_markup_table() (in module tcren.project2d.tables) residue_pair_types() (in module tcren.contact_types) residue_rotamers() (in module tcren.energetics.rotamers) residue_torsions() (in module tcren.torsions) residues (tcren.structure.model.Chain attribute) (tcren.structure.model.RegionMarkup attribute) resname (tcren.stacking.Ring attribute) (tcren.structure.model.Residue attribute) resolve_sources() (in module tcren.structure.io) resolve_structure_ids() (in module tcren.structure.io) response_matrix() (in module tcren.cpl) ResponseMatrix (class in tcren.cpl) rest (tcren.mechanics.springs.InterfaceSprings attribute) reversed_dock (tcren.docking.frame.CanonResult attribute) RIDGE_PERCENTILE (in module tcren.topology.surface) Ring (class in tcren.stacking) RING_ATOMS (in module tcren.stacking) ring_of() (in module tcren.stacking) ring_pair() (in module tcren.stacking) ring_stacking() (in module tcren.stacking) RingPair (class in tcren.stacking) rings() (in module tcren.stacking) rmsd (tcren.docking.align.OrientationResult attribute) (tcren.docking.frame.CanonResult attribute) (tcren.pipeline.PipelineResult attribute) (tcren.project2d.frame.ProjectionResult attribute) rmsf (tcren.mechanics.dynamics.Stability attribute) ROLES (in module tcren.potts) roles (tcren.potts.PottsModel attribute) rotation (tcren.docking.align.OrientationResult attribute) (tcren.docking.frame.CanonResult attribute) row_of() (tcren.cpl.ResponseMatrix method) rows (tcren.potential.aaindex.AAindexEntry attribute) run() (in module tcren.pipeline) (tcren.refine.engines.base.Engine method) (tcren.refine.engines.ccd.CcdEngine method) (tcren.refine.engines.dope.DopeEngine method) (tcren.refine.engines.openmm_engine.OpenMMEngine method) (tcren.refine.engines.promod3_engine.ProMod3Engine method) run_folder() (in module tcren.docking.pipeline) run_shuffle() (in module tcren.shuffle) run_superimpose() (in module tcren.docking.pipeline) rupture() (in module tcren.mechanics.springs) S s_score() (in module tcren.reliability) sample_maps() (in module tcren.potts) scale (tcren.score.transform.Transformer attribute) (tcren.topology.surface.SurfaceMap attribute) scale() (tcren.potential.model.Potential method) score (tcren.annotation.cgene.ConstantCall attribute) (tcren.mhc.linker.MhcAlignmentCheck attribute) score() (in module tcren.cli) score_peptides() (in module tcren.energetics.scoring) score_records() (in module tcren.annotation.arda_adapter) score_row() (in module tcren.pipeline) score_sites() (in module tcren.potts) score_structure() (in module tcren.potts) score_structures() (in module tcren.energetics.scoring) score_table() (in module tcren.score) ScoreModel (class in tcren.score) scores (tcren.pipeline.PipelineResult attribute) scoring() (in module tcren.cli) screening_yield() (in module tcren.reliability) select_primary_complex() (in module tcren.docking.chains) seq_index (tcren.stacking.Ring attribute) (tcren.structure.model.Residue attribute) sequence (tcren.mhc.imgt.MhcAllele attribute) (tcren.structure.model.RegionMarkup attribute) sequence() (tcren.structure.model.Chain method) shift_u (tcren.docking.angles.TcrPlacement attribute) shift_w (tcren.docking.angles.TcrPlacement attribute) short (tcren.viz.pymol.Axis attribute) shuffle() (in module tcren.cli) side (tcren.energetics.scoring.RecognitionMatrix attribute) (tcren.topology.surface.SurfaceMap attribute) sidecar_path() (in module tcren.provenance) sigma_sum (tcren.contactmap.ModeCentroid attribute) SIGNED_CHANNELS (in module tcren.viz.surface2d) site_codes() (in module tcren.potts) SMOOTH_INTERFACES (in module tcren.energetics.mutation) smoothed_reference() (in module tcren.energetics.mutation) soft_energy() (in module tcren.energetics.rotamers) source (tcren.topology.surface.SurfaceMap attribute) span_saturation() (in module tcren.geometry) species (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) split_linked_peptides() (in module tcren.mhc.linker) Stability (class in tcren.mechanics.dynamics) stability_table() (in module tcren.mechanics.dynamics) StabilityReport (class in tcren.mechanics.stability) STACK_CENTROID_MAX (in module tcren.contact_types) stacked_pairs() (in module tcren.contact_types) StaleTableError stamp() (in module tcren.provenance) start_seq_index (tcren.structure.model.RegionMarkup attribute) STATUS (in module tcren.descriptors.catalogue) stiffness_tensor() (in module tcren.mechanics.springs) STRAIN_TERMS (in module tcren.cohort) strain_z() (in module tcren.cohort) Structure (class in tcren.structure.model) structure (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) structure_id (tcren.cpl.ResponseMatrix attribute) (tcren.mechanics.dynamics.Stability attribute) (tcren.topology.surface.SurfaceMap attribute) structure_id_from_path() (in module tcren.structure.io) structure_output_path() (in module tcren.structure.io) structure_paths() (in module tcren.structure.io) structure_stem() (in module tcren.structure.io) substitute_peptide() (in module tcren.refine) (in module tcren.refine.substitute) substitute_residues() (in module tcren.refine.substitute) substitute_tcr() (in module tcren.docking.graft) substitute_tcr_cmd() (in module tcren.cli) summarize_structure() (in module tcren.oracle) superimpose() (in module tcren.cli) (in module tcren.docking.superimpose) surface() (in module tcren.cli) surface_complementarity() (in module tcren.topology.surface) surface_distance() (in module tcren.topology.surface) surface_features() (in module tcren.topology.literature) surface_map() (in module tcren.topology.surface) surface_stats() (in module tcren.topology.surface) surface_table() (in module tcren.topology.surface) surface_tree() (in module tcren.topology.surface) SurfaceMap (class in tcren.topology.surface) suspect (tcren.refine.register.RegisterReport property) (tcren.refine.RegisterReport property) symmetric (tcren.potential.aaindex.AAindexEntry property) symmetrize() (in module tcren.contacts.table) symmetrize_counts() (in module tcren.potential.derive) T T_FEATURES_TOPO (in module tcren.reliability) t_score() (in module tcren.reliability) T_SIGNS (in module tcren.reliability) tcr_alanine_reference() (in module tcren.energetics.mutation) tcr_alanine_scan() (in module tcren.energetics.mutation) tcr_facing (tcren.refine.anchors.Decomposition attribute) (tcren.refine.Decomposition attribute) tcr_peptide() (tcren.contactmap.ContactMap method) tcr_placement() (in module tcren.docking.angles) TCR_PLACEMENT_FEATURES (in module tcren.descriptors.catalogue) TCR_REGIONS (in module tcren.contactmap) tcr_unit_y (tcren.docking.tcrdock_geometry.DockingGeometry attribute) tcr_unit_z (tcren.docking.tcrdock_geometry.DockingGeometry attribute) tcren() (in module tcren.potential.model) tcren.analysis module tcren.annotation.arda_adapter module tcren.annotation.batch module tcren.annotation.cgene module tcren.annotation.chains module tcren.binder module tcren.binder.noise module tcren.clashes module tcren.cli module tcren.cohort module tcren.contact_types module tcren.contactmap module tcren.contacts.definitions module tcren.contacts.geometry module tcren.contacts.table module tcren.cpl module tcren.descriptors module tcren.descriptors.catalogue module tcren.descriptors.compute module tcren.descriptors.table module tcren.docking.align module tcren.docking.angles module tcren.docking.chains module tcren.docking.exceptions module tcren.docking.frame module tcren.docking.graft module tcren.docking.pipeline module tcren.docking.superimpose module tcren.docking.tcrdock_geometry module tcren.energetics module tcren.energetics.mutation module tcren.energetics.rotamers module tcren.energetics.scoring module tcren.geometry module tcren.mechanics module tcren.mechanics.dynamics module tcren.mechanics.springs module tcren.mechanics.stability module tcren.metadata module tcren.mhc.domains module tcren.mhc.imgt module tcren.mhc.linker module tcren.mhc.mapper module tcren.mhc.pseudo module tcren.mhc.reference module tcren.mhc.regions module tcren.oracle module tcren.paper.bootstrap module tcren.paper.helpers module tcren.paths module tcren.pipeline module tcren.potential.aaindex module tcren.potential.derive module tcren.potential.model module tcren.potential.redundancy module tcren.potts module tcren.project2d.frame module tcren.project2d.pockets module tcren.project2d.tables module tcren.provenance module tcren.recent module tcren.recognition module tcren.refine module tcren.refine.anchors module tcren.refine.engines.base module tcren.refine.engines.ccd module tcren.refine.engines.dope module tcren.refine.engines.openmm_engine module tcren.refine.engines.promod3_engine module tcren.refine.interface module tcren.refine.model module tcren.refine.oracle_flexpep module tcren.refine.register module tcren.refine.rmsd module tcren.refine.substitute module tcren.score.fit module tcren.score.model module tcren.score.transform module tcren.scoring_rank module tcren.shuffle module tcren.stacking module tcren.structure.io module tcren.structure.model module tcren.topology module tcren.topology.footprint module tcren.topology.graph module tcren.topology.literature module tcren.topology.pose module tcren.topology.surface module tcren.torsions module tcren.viz.palette module tcren.viz.pocket3d module tcren.viz.pymol module tcren.viz.surface2d module tcren.viz.svg2d module tcren2() (in module tcren.potential.model) tcren_home() (in module tcren.paths) TcrPlacement (class in tcren.docking.angles) tend (tcren.mhc.mapper.MhcCall attribute) tidy_contacts() (in module tcren.contacts.table) tilt_mean() (in module tcren.potts) title (tcren.potential.aaindex.AAindexEntry attribute) to_csv() (tcren.contactmap.ContactMap method) (tcren.potential.model.Potential method) to_dict() (tcren.docking.tcrdock_geometry.DockingGeometry method) (tcren.mechanics.dynamics.Stability method) to_frame() (tcren.cpl.ResponseMatrix method) (tcren.topology.surface.SurfaceMap method) to_json() (tcren.potts.PottsModel method) to_potential() (tcren.potential.aaindex.AAindexEntry method) torsion (tcren.docking.tcrdock_geometry.DockingGeometry attribute) torsions (tcren.geometry.LoopInternalCoords attribute) transform() (tcren.score.transform.Transformer method) transform_names() (tcren.score.transform.Transformer method) Transformer (class in tcren.score.transform) translation (tcren.docking.align.OrientationResult attribute) (tcren.docking.frame.CanonResult attribute) tstart (tcren.mhc.mapper.MhcCall attribute) type_weights() (in module tcren.contact_types) TYPES_V1 (in module tcren.contact_types) TYPES_V2 (in module tcren.contact_types) U U1 (tcren.score.model.Joint attribute) UNTYPED (in module tcren.contact_types) uv (tcren.project2d.frame.ProjectionResult property) V value() (tcren.potential.model.HydrophobicityFit method) (tcren.potential.model.Potential method) vertical (tcren.stacking.RingPair attribute) view_pocket_cdr() (in module tcren.viz.pocket3d) virtual_cb() (in module tcren.refine.substitute) W WEIGHTS (in module tcren.mechanics.springs) wild_type_at() (tcren.cpl.ResponseMatrix method) working_set() (in module tcren.score.transform) worst (tcren.clashes.ClashReport attribute) write_pdb() (in module tcren.structure.io) write_structure() (in module tcren.structure.io) wrong_register (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) Y y_alpha (tcren.contactmap.ModeCentroid attribute) y_beta (tcren.contactmap.ModeCentroid attribute) Z zscore() (in module tcren.cohort)