Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Y | Z A a (tcren.mechanics.InterfaceSprings attribute) aa (tcren.cpl.ResponseMatrix attribute) (tcren.scoring.RecognitionMatrix attribute) (tcren.structure.model.Residue attribute) AA20 (in module tcren.cpl) (in module tcren.potential.model) AA21 (in module tcren.potential.model) alanine_scan() (in module tcren.ddg) align_to_canonical() (in module tcren.orient.pipeline) align_to_native() (in module tcren.orient.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) alphabet (tcren.potential.model.Potential 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.paper.helpers) 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.paper.helpers) annotate_tcr_chains() (in module tcren.annotation.arda_adapter) annotate_tcr_chains_scored() (in module tcren.annotation.arda_adapter) 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.orient.align) as_matrix() (tcren.potential.model.Potential method) Atom (class in tcren.structure.model) atoms (tcren.structure.model.Residue 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) Axis (class in tcren.viz.pymol) axis (tcren.mechanics.InterfaceSprings attribute) B b (tcren.mechanics.InterfaceSprings attribute) backbone_rmsd (tcren.refine.PeptideRMSD attribute) (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) (tcren.refine.rmsd.PeptideRMSD attribute) background_peptides() (in module tcren.scoring_rank) BayesianLogisticRecognizer (class in tcren.recognition) best_ref (tcren.mhc.linker.MhcAlignmentCheck attribute) binder() (in module tcren.cli) binder_score() (in module tcren.binder) 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) build() (in module tcren.mhc.reference) build_canonical_frame() (in module tcren.orient.frame) build_mhc_ref() (in module tcren.cli) by_partner (tcren.clashes.ClashReport attribute) by_seq_index() (tcren.structure.model.Chain method) by_type() (tcren.structure.model.Structure method) C 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.orient.frame) canonical_groove() (in module tcren.mhc.domains) canonicalize_structure() (in module tcren.orient.pipeline) CanonResult (class in tcren.orient.frame) 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) cell_type (tcren.annotation.cgene.ConstantCall attribute) (tcren.orient.docking.DockingAngles attribute) (tcren.structure.model.Structure attribute) cell_type() (in module tcren.annotation.cgene) 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.structure.model.Chain attribute) chain_map (tcren.orient.frame.CanonResult attribute) chain_role (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) chain_supertype (tcren.structure.model.Chain attribute) chain_type (tcren.structure.model.Chain attribute) chains (tcren.structure.model.Structure attribute) check_against_mhc() (in module tcren.mhc.linker) check_oriented_complex() (in module tcren.orient.pipeline) check_register() (in module tcren.refine) (in module tcren.refine.register) 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) 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) cluster_weights() (in module tcren.potential.redundancy) color_for() (in module tcren.viz.palette) column_of() (tcren.cpl.ResponseMatrix method) compare() (in module tcren.paper.helpers) compare_potentials() (in module tcren.analysis) complex_species (tcren.structure.model.Structure attribute) composite() (in module tcren.viz.pymol) constant_span() (in module tcren.annotation.cgene) ConstantCall (class in tcren.annotation.cgene) contact_stability() (in module tcren.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) 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) coupling() (in module tcren.cohort) coupling_residues() (in module tcren.mechanics) cpl_cmd() (in module tcren.cli) crossing_angle (tcren.orient.docking.DockingAngles attribute) crossing_angle_signed (tcren.orient.docking.DockingAngles attribute) crossing_incident_from_vector() (in module tcren.orient.docking) D d (tcren.orient.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) ddg() (in module tcren.ddg) ddg_cmd() (in module tcren.cli) decision_function() (tcren.recognition.BayesianLogisticRecognizer method) (tcren.recognition.GaussianBNClassifier method) decompose() (in module tcren.refine.anchors) Decomposition (class in tcren.refine) (class in tcren.refine.anchors) definition (tcren.viz.pymol.Axis attribute) derive_potential() (in module tcren.cli) derive_tcren() (in module tcren.potential.derive) derive_tcren_loo() (in module tcren.potential.derive) DESCRIPTORS (in module tcren.recognition) descriptors() (in module tcren.recognition) detect_linked_peptide() (in module tcren.mhc.linker) detect_reverse_dock() (in module tcren.orient.exceptions) discover_similar() (in module tcren.recent) docking_angles() (in module tcren.orient.docking) docking_geometry() (in module tcren.orient.tcrdock_geometry) DockingAngles (class in tcren.orient.docking) DockingGeometry (class in tcren.orient.tcrdock_geometry) DopeEngine (class in tcren.refine.engines.dope) download_human() (in module tcren.mhc.imgt) download_mouse() (in module tcren.mhc.imgt) E element (tcren.structure.model.Atom attribute) encode_features() (in module tcren.recognition) end_seq_index (tcren.structure.model.RegionMarkup attribute) energy (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) (tcren.scoring.RecognitionMatrix attribute) energy() (in module tcren.cli) Engine (class in tcren.refine.engines.base) engine (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) EngineUnavailable equimolar_effect() (in module tcren.cpl) exp_lost (tcren.stability.StabilityReport attribute) extra (tcren.pipeline.PipelineResult attribute) F f_invert_by_iptm() (in module tcren.cohort) f_score() (in module tcren.cohort) F_TERMS (in module tcren.cohort) 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) fit() (tcren.recognition.GaussianBNClassifier method) 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_width_alpha (tcren.contactmap.ModeCentroid attribute) footprint_width_beta (tcren.contactmap.ModeCentroid attribute) FORCED_POSE_MODEL (in module tcren.recognition) forced_pose_score() (in module tcren.recognition) frac_marg_lt1 (tcren.stability.StabilityReport attribute) frac_robust (tcren.stability.StabilityReport attribute) frame (tcren.orient.frame.CanonResult attribute) (tcren.project2d.frame.ProjectionResult attribute) from_csv() (tcren.potential.model.Potential class method) from_dict() (tcren.recognition.BayesianLogisticRecognizer class method) (tcren.recognition.GaussianBNClassifier class method) from_structure() (tcren.contactmap.ContactMap class method) frozen_recognizers() (in module tcren.recognition) FULL_FEATURES (in module tcren.recognition) G GaussianBNClassifier (class in tcren.recognition) gene (tcren.annotation.cgene.ConstantCall attribute) gizmo_cgo() (in module tcren.viz.pymol) gizmo_scene() (in module tcren.viz.pymol) graft_tcr() (in module tcren.shuffle) groove_for() (in module tcren.mhc.domains) 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 has_clashes() (in module tcren.clashes) height (tcren.project2d.frame.ProjectionResult property) I identity (tcren.mhc.mapper.MhcCall attribute) import_structure() (in module tcren.structure.io) importance_scene() (in module tcren.viz.pymol) incident_angle (tcren.orient.docking.DockingAngles 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.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) interface_scene() (in module tcren.viz.pymol) interface_springs() (in module tcren.mechanics) INTERFACE_SYMMETRY_FEATURES (in module tcren.recognition) INTERFACES (in module tcren.cpl) InterfaceSprings (class in tcren.mechanics) is_mhc (tcren.mhc.linker.MhcAlignmentCheck property) is_real_interface() (in module tcren.binder) is_structure_file() (in module tcren.structure.io) iter_structures() (in module tcren.structure.io) iterations (tcren.refine.engines.base.ModelResult attribute) (tcren.refine.model.ModelResult attribute) K k (tcren.mechanics.InterfaceSprings attribute) keskin() (in module tcren.potential.model) keys (tcren.project2d.frame.ProjectionResult attribute) kit_score() (in module tcren.recognition) L label (tcren.viz.pymol.Axis attribute) label_points() (in module tcren.viz.pymol) letter (tcren.viz.pymol.Axis attribute) load() (tcren.recognition.BayesianLogisticRecognizer class method) (tcren.recognition.GaussianBNClassifier class method) load_interface_contacts() (in module tcren.analysis) locus (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) LoopInternalCoords (class in tcren.geometry) M make_decoys() (in module tcren.shuffle) map_mhc() (in module tcren.mhc.mapper) marginal_decision() (tcren.recognition.GaussianBNClassifier method) marginal_proba() (tcren.recognition.GaussianBNClassifier method) markup (tcren.pipeline.PipelineResult attribute) matrix (tcren.potential.model.Potential attribute) max_overlap (tcren.clashes.ClashReport attribute) mean_margin (tcren.stability.StabilityReport attribute) mechanics() (in module tcren.cli) mhc_annotation() (in module tcren.paper.helpers) mhc_calls (tcren.pipeline.PipelineResult 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_unit_y (tcren.orient.tcrdock_geometry.DockingGeometry attribute) mhc_unit_z (tcren.orient.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) mj() (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.cgene tcren.annotation.chains tcren.binder tcren.clashes tcren.cli tcren.cohort tcren.contact_types tcren.contactmap tcren.contacts.definitions tcren.contacts.geometry tcren.contacts.table tcren.cpl tcren.ddg tcren.geometry tcren.mechanics tcren.mhc.domains tcren.mhc.imgt tcren.mhc.linker tcren.mhc.mapper tcren.mhc.pseudo tcren.mhc.reference tcren.mhc.regions tcren.oracle tcren.orient.align tcren.orient.chains tcren.orient.docking tcren.orient.exceptions tcren.orient.frame tcren.orient.graft tcren.orient.pipeline tcren.orient.superimpose tcren.orient.tcrdock_geometry tcren.paper.bootstrap tcren.paper.helpers tcren.paths tcren.pipeline tcren.potential.derive tcren.potential.model tcren.potential.redundancy tcren.project2d.frame tcren.project2d.pockets tcren.project2d.tables 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.scoring tcren.scoring_rank tcren.shuffle tcren.stability tcren.structure.io tcren.structure.model tcren.viz.palette tcren.viz.pocket3d tcren.viz.pymol tcren.viz.svg2d multi_contacts() (in module tcren.contacts.definitions) mutation_effect() (in module tcren.cpl) N n_anchor_atoms (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult 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_clashes (tcren.clashes.ClashReport attribute) n_contacts (tcren.stability.StabilityReport attribute) n_contacts_alpha (tcren.contactmap.ModeCentroid attribute) n_contacts_beta (tcren.contactmap.ModeCentroid attribute) n_peptide_atoms (tcren.clashes.ClashReport attribute) n_severe (tcren.clashes.ClashReport attribute) n_term_extra (tcren.mhc.linker.MhcAlignmentCheck attribute) n_va (tcren.orient.docking.DockingAngles attribute) n_vb (tcren.orient.docking.DockingAngles attribute) name (tcren.potential.model.Potential 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) 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) neoantigen_ddg() (in module tcren.ddg) nonredundant_ids() (in module tcren.potential.redundancy) O OpenMMEngine (class in tcren.refine.engines.openmm_engine) orient() (in module tcren.cli) OrientationResult (class in tcren.orient.align) oriented (tcren.pipeline.PipelineResult attribute) overlap (tcren.clashes.ClashPair attribute) overlay_scene() (in module tcren.viz.pymol) P PALETTES (in module tcren.viz.pymol) paper_bootstrap() (in module tcren.cli) 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) 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.refine.anchors.Decomposition attribute) (tcren.refine.Decomposition attribute) peptide_length (tcren.contactmap.ContactMap attribute) peptide_residue (tcren.clashes.ClashPair attribute) peptide_rmsd() (in module tcren.refine) (in module tcren.refine.rmsd) PeptideRMSD (class in tcren.refine) (class in tcren.refine.rmsd) percentile_rank() (in module tcren.scoring_rank) phi (tcren.cpl.ResponseMatrix attribute) phi_bind() (in module tcren.cohort) phi_mhc (tcren.cpl.ResponseMatrix attribute) phi_tcr (tcren.cpl.ResponseMatrix attribute) pipeline() (in module tcren.cli) PipelineResult (class in tcren.pipeline) pocket_markers() (in module tcren.project2d.pockets) position_distribution() (in module tcren.analysis) position_scan() (in module tcren.cpl) positions (tcren.cpl.ResponseMatrix attribute) (tcren.scoring.RecognitionMatrix attribute) Potential (class in tcren.potential.model) potential_long() (in module tcren.analysis) potential_matrix() (in module tcren.analysis) predict_anchors() (in module tcren.refine) (in module tcren.refine.anchors) predict_proba() (tcren.recognition.BayesianLogisticRecognizer method) (tcren.recognition.GaussianBNClassifier method) presentation (tcren.refine.anchors.Decomposition attribute) (tcren.refine.Decomposition attribute) probe_rotation() (in module tcren.viz.pymol) project_structure() (in module tcren.project2d.frame) ProjectionResult (class in tcren.project2d.frame) ProMod3Engine (class in tcren.refine.engines.promod3_engine) pyrosetta_available() (in module tcren.refine.oracle_flexpep) Q q_coupled() (in module tcren.cohort) q_f() (in module tcren.cohort) q_f_iptm() (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_iptm() (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 rank() (in module tcren.cli) reach_max() (in module tcren.geometry) reachability_floor() (in module tcren.geometry) real_probability() (in module tcren.recognition) reason (tcren.refine.register.RegisterReport attribute) (tcren.refine.RegisterReport attribute) recent_dir() (in module tcren.recent) RECOGNITION_FEATURES (in module tcren.recognition) recognition_features() (in module tcren.recognition) recognition_matrix() (in module tcren.scoring) recognition_table() (in module tcren.recognition) RecognitionMatrix (class in tcren.scoring) recognize() (in module tcren.cli) reference_db() (in module tcren.mhc.reference) reference_delta() (in module tcren.ddg) reference_fasta() (in module tcren.mhc.reference) reference_id (tcren.orient.align.OrientationResult attribute) (tcren.orient.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 (tcren.structure.model.Chain attribute) registered_map() (in module tcren.contactmap) RegisterReport (class in tcren.refine) (class in tcren.refine.register) rename_chains() (in module tcren.orient.chains) render() (in module tcren.viz.pymol) render_complementarity_map() (in module tcren.viz.svg2d) representative_atom_contacts() (in module tcren.contacts.geometry) Residue (class in tcren.structure.model) residue_annotation() (in module tcren.contacts.table) residue_importance() (in module tcren.viz.pymol) residue_markup_table() (in module tcren.project2d.tables) residues (tcren.structure.model.Chain attribute) (tcren.structure.model.RegionMarkup attribute) resname (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.InterfaceSprings attribute) reversed_dock (tcren.orient.frame.CanonResult attribute) rmsd (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult attribute) (tcren.pipeline.PipelineResult attribute) (tcren.project2d.frame.ProjectionResult attribute) rotation (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult attribute) row_of() (tcren.cpl.ResponseMatrix method) 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.orient.pipeline) run_shuffle() (in module tcren.shuffle) run_superimpose() (in module tcren.orient.pipeline) rupture() (in module tcren.mechanics) S save() (tcren.recognition.BayesianLogisticRecognizer method) (tcren.recognition.GaussianBNClassifier method) score (tcren.annotation.cgene.ConstantCall attribute) (tcren.mhc.linker.MhcAlignmentCheck attribute) score() (in module tcren.cli) score_peptides() (in module tcren.scoring) score_records() (in module tcren.annotation.arda_adapter) score_row() (in module tcren.pipeline) score_structures() (in module tcren.scoring) scores (tcren.pipeline.PipelineResult attribute) scoring() (in module tcren.cli) select_primary_complex() (in module tcren.orient.chains) seq_index (tcren.structure.model.Residue attribute) sequence (tcren.mhc.imgt.MhcAllele attribute) (tcren.structure.model.RegionMarkup attribute) sequence() (tcren.structure.model.Chain method) short (tcren.viz.pymol.Axis attribute) shuffle() (in module tcren.cli) side (tcren.scoring.RecognitionMatrix attribute) sigma_sum (tcren.contactmap.ModeCentroid 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) StabilityReport (class in tcren.stability) start_seq_index (tcren.structure.model.RegionMarkup attribute) stiffness_tensor() (in module tcren.mechanics) 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) 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_tcr() (in module tcren.orient.graft) substitute_tcr_cmd() (in module tcren.cli) summarize_structure() (in module tcren.oracle) superimpose() (in module tcren.cli) (in module tcren.orient.superimpose) suspect (tcren.refine.register.RegisterReport property) (tcren.refine.RegisterReport property) symmetrize() (in module tcren.contacts.table) symmetrize_counts() (in module tcren.potential.derive) T tcr_facing (tcren.refine.anchors.Decomposition attribute) (tcren.refine.Decomposition attribute) tcr_peptide() (tcren.contactmap.ContactMap method) TCR_REGIONS (in module tcren.contactmap) tcr_unit_y (tcren.orient.tcrdock_geometry.DockingGeometry attribute) tcr_unit_z (tcren.orient.tcrdock_geometry.DockingGeometry attribute) tcren() (in module tcren.potential.model) tcren.analysis module tcren.annotation.arda_adapter module tcren.annotation.cgene module tcren.annotation.chains module tcren.binder 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.ddg module tcren.geometry module tcren.mechanics 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.orient.align module tcren.orient.chains module tcren.orient.docking module tcren.orient.exceptions module tcren.orient.frame module tcren.orient.graft module tcren.orient.pipeline module tcren.orient.superimpose module tcren.orient.tcrdock_geometry module tcren.paper.bootstrap module tcren.paper.helpers module tcren.paths module tcren.pipeline module tcren.potential.derive module tcren.potential.model module tcren.potential.redundancy module tcren.project2d.frame module tcren.project2d.pockets module tcren.project2d.tables 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.scoring module tcren.scoring_rank module tcren.shuffle module tcren.stability module tcren.structure.io module tcren.structure.model module tcren.viz.palette module tcren.viz.pocket3d module tcren.viz.pymol module tcren.viz.svg2d module tend (tcren.mhc.mapper.MhcCall attribute) tidy_contacts() (in module tcren.contacts.table) to_csv() (tcren.contactmap.ContactMap method) (tcren.potential.model.Potential method) to_dict() (tcren.orient.tcrdock_geometry.DockingGeometry method) (tcren.recognition.BayesianLogisticRecognizer method) (tcren.recognition.GaussianBNClassifier method) to_dot() (tcren.recognition.GaussianBNClassifier method) to_frame() (tcren.cpl.ResponseMatrix method) torsion (tcren.orient.tcrdock_geometry.DockingGeometry attribute) torsions (tcren.geometry.LoopInternalCoords attribute) translation (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult attribute) tstart (tcren.mhc.mapper.MhcCall attribute) U uv (tcren.project2d.frame.ProjectionResult property) V value() (tcren.potential.model.Potential method) view_pocket_cdr() (in module tcren.viz.pocket3d) W WEIGHTS (in module tcren.mechanics) wild_type_at() (tcren.cpl.ResponseMatrix method) 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)