Index A | B | C | D | E | F | G | I | K | L | M | N | O | P | Q | R | S | T | V | W A aa (tcren.structure.model.Residue attribute) AA20 (in module tcren.potential.model) AA21 (in module tcren.potential.model) 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) annotate() (in module tcren.cli) 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_tcr_chains() (in module tcren.annotation.arda_adapter) annotate_tcr_chains_scored() (in module tcren.annotation.arda_adapter) 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) B best_ref (tcren.mhc.linker.MhcAlignmentCheck attribute) bits (tcren.mhc.mapper.MhcCall attribute) build() (in module tcren.mhc.reference) build_canonical_frame() (in module tcren.orient.frame) build_mhc_ref() (in module tcren.cli) 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_distance_matrix() (in module tcren.contacts.geometry) calls_from_hits() (in module tcren.mhc.mapper) 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) 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_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) cif_lines() (in module tcren.structure.io) cigar (tcren.mhc.mapper.MhcCall attribute) classify_chain_constant() (in module tcren.annotation.cgene) classify_chains() (in module tcren.annotation.chains) classify_constants() (in module tcren.annotation.cgene) compare_potentials() (in module tcren.analysis) complex_species (tcren.structure.model.Structure attribute) constant_span() (in module tcren.annotation.cgene) ConstantCall (class in tcren.annotation.cgene) 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) coord (tcren.structure.model.Atom attribute) 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 d1 (tcren.contacts.definitions.ContactDefinition attribute) d2 (tcren.contacts.definitions.ContactDefinition attribute) d3 (tcren.contacts.definitions.ContactDefinition attribute) data_dir() (in module tcren.paths) derive_potential() (in module tcren.cli) derive_tcren() (in module tcren.potential.derive) derive_tcren_loo() (in module tcren.potential.derive) detect_linked_peptide() (in module tcren.mhc.linker) detect_reverse_dock() (in module tcren.orient.exceptions) docking_angles() (in module tcren.orient.docking) DockingAngles (class in tcren.orient.docking) download_human() (in module tcren.mhc.imgt) download_mouse() (in module tcren.mhc.imgt) E element (tcren.structure.model.Atom attribute) end_seq_index (tcren.structure.model.RegionMarkup attribute) extra (tcren.pipeline.PipelineResult attribute) F fetch_data() (in module tcren.cli) fetch_recent() (in module tcren.cli) frame (tcren.orient.frame.CanonResult attribute) from_csv() (tcren.potential.model.Potential class method) from_structure() (tcren.contactmap.ContactMap class method) G gene (tcren.annotation.cgene.ConstantCall attribute) groove_for() (in module tcren.mhc.domains) I identity (tcren.mhc.mapper.MhcCall attribute) import_structure() (in module tcren.structure.io) incident_angle (tcren.orient.docking.DockingAngles attribute) info() (in module tcren.cli) insertion_code (tcren.structure.model.Residue attribute) interface() (tcren.contactmap.ContactMap method) is_mhc (tcren.mhc.linker.MhcAlignmentCheck property) is_structure_file() (in module tcren.structure.io) iter_structures() (in module tcren.structure.io) K keskin() (in module tcren.potential.model) L load_interface_contacts() (in module tcren.analysis) locus (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) M map_mhc() (in module tcren.mhc.mapper) markup (tcren.pipeline.PipelineResult attribute) matrix (tcren.potential.model.Potential attribute) mhc_calls (tcren.pipeline.PipelineResult attribute) mhc_class (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall 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) module tcren.analysis tcren.annotation.arda_adapter tcren.annotation.cgene tcren.annotation.chains tcren.cli tcren.contactmap tcren.contacts.definitions tcren.contacts.geometry tcren.contacts.table tcren.mhc.domains tcren.mhc.imgt tcren.mhc.linker tcren.mhc.mapper tcren.mhc.pseudo tcren.mhc.reference tcren.mhc.regions tcren.orient.align tcren.orient.chains tcren.orient.docking tcren.orient.exceptions tcren.orient.frame tcren.orient.pipeline tcren.paths tcren.pipeline tcren.potential.derive tcren.potential.model tcren.refine tcren.refine.substitute tcren.scoring tcren.structure.io tcren.structure.model multi_contacts() (in module tcren.contacts.definitions) N n_anchor_atoms (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult 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.structure.model.Atom attribute) native_dir() (in module tcren.paths) O orient() (in module tcren.cli) OrientationResult (class in tcren.orient.align) oriented (tcren.pipeline.PipelineResult attribute) P 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) 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_length (tcren.contactmap.ContactMap attribute) pipeline() (in module tcren.cli) PipelineResult (class in tcren.pipeline) position_distribution() (in module tcren.analysis) Potential (class in tcren.potential.model) potential_long() (in module tcren.analysis) potential_matrix() (in module tcren.analysis) Q 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 reference_db() (in module tcren.mhc.reference) reference_fasta() (in module tcren.mhc.reference) reference_id (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult attribute) reference_structure_path() (in module tcren.paths) refine() (in module tcren.cli) refine_peptide() (in module tcren.refine) region_contact_counts() (in module tcren.analysis) region_type (tcren.structure.model.RegionMarkup attribute) RegionMarkup (class in tcren.structure.model) regions (tcren.structure.model.Chain attribute) rename_chains() (in module tcren.orient.chains) representative_atom_contacts() (in module tcren.contacts.geometry) Residue (class in tcren.structure.model) residue_annotation() (in module tcren.contacts.table) residues (tcren.structure.model.Chain attribute) (tcren.structure.model.RegionMarkup attribute) resname (tcren.structure.model.Residue attribute) reversed_dock (tcren.orient.frame.CanonResult attribute) rmsd (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult attribute) (tcren.pipeline.PipelineResult attribute) rotation (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult attribute) run() (in module tcren.pipeline) run_folder() (in module tcren.orient.pipeline) run_superimpose() (in module tcren.orient.pipeline) S 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) 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) species (tcren.mhc.imgt.MhcAllele attribute) (tcren.mhc.mapper.MhcCall attribute) split_linked_peptides() (in module tcren.mhc.linker) start_seq_index (tcren.structure.model.RegionMarkup attribute) Structure (class in tcren.structure.model) structure_id_from_path() (in module tcren.structure.io) structure_output_path() (in module tcren.structure.io) structure_paths() (in module tcren.structure.io) substitute_peptide() (in module tcren.refine) (in module tcren.refine.substitute) superimpose() (in module tcren.cli) symmetrize() (in module tcren.contacts.table) T tcr_peptide() (tcren.contactmap.ContactMap method) tcren() (in module tcren.potential.model) tcren.analysis module tcren.annotation.arda_adapter module tcren.annotation.cgene module tcren.annotation.chains module tcren.cli module tcren.contactmap module tcren.contacts.definitions module tcren.contacts.geometry module tcren.contacts.table 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.orient.align module tcren.orient.chains module tcren.orient.docking module tcren.orient.exceptions module tcren.orient.frame module tcren.orient.pipeline module tcren.paths module tcren.pipeline module tcren.potential.derive module tcren.potential.model module tcren.refine module tcren.refine.substitute module tcren.scoring module tcren.structure.io module tcren.structure.model 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) translation (tcren.orient.align.OrientationResult attribute) (tcren.orient.frame.CanonResult attribute) tstart (tcren.mhc.mapper.MhcCall attribute) V value() (tcren.potential.model.Potential method) W write_pdb() (in module tcren.structure.io) write_structure() (in module tcren.structure.io)