Index

A

abTCR (class in stcrpy.tcr_processing.TCR) Accept (class in stcrpy.tcr_processing.utils.region_definitions) accept() (stcrpy.tcr_processing.Select.select_all method) (stcrpy.tcr_processing.utils.region_definitions.Accept method) accept_atom() (stcrpy.tcr_processing.Select.backbone method) (stcrpy.tcr_processing.Select.select_all method) accept_chain() (stcrpy.tcr_processing.Select.select_all method) accept_fragment() (stcrpy.tcr_processing.Select.select_all method) accept_holder() (stcrpy.tcr_processing.Select.select_all method) (stcrpy.tcr_processing.Select.variable_only method) accept_model() (stcrpy.tcr_processing.Select.select_all method) accept_residue() (stcrpy.tcr_processing.Select.cdr3 method) (stcrpy.tcr_processing.Select.select_all method) (stcrpy.tcr_processing.Select.variable_only method) add() (stcrpy.tcr_processing.Fragment.Fragment method) add_com() (stcrpy.tcr_geometry.TCRCoM.TCRCoM method)

add_positions() (stcrpy.tcr_processing.utils.region_definitions.Accept method) add_regions() (stcrpy.tcr_processing.utils.region_definitions.Accept method) add_unnumbered() (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCRchain.TCRchain method) AGchain (class in stcrpy.tcr_processing.AGchain) align_by_mhc() (stcrpy.tcr_metrics.tcr_interface_rmsd.InterfaceRMSD method) align_numbering() (in module stcrpy.tcr_processing.annotate) align_scTCR_numbering() (in module stcrpy.tcr_processing.annotate) analyse() (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCRchain.TCRchain method) analyse_tcrs() (in module stcrpy.tcr_methods.tcr_batch_operations) angle() (in module stcrpy.tcr_processing.utils.common) annotate() (in module stcrpy.tcr_processing.annotate) annotate_children() (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCRchain.TCRchain method) annotate_regions() (in module stcrpy.tcr_processing.utils.region_definitions)

B

backbone (class in stcrpy.tcr_processing.Select) batch_load_TCRs() (in module stcrpy.tcr_methods.tcr_batch_operations)

batch_yield_TCRs() (in module stcrpy.tcr_methods.tcr_batch_operations) build_graph() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphConstructor method)

C

calculate_centres_of_mass() (stcrpy.tcr_geometry.TCRCoM.TCRCoM method) calculate_docking_angle() (stcrpy.tcr_geometry.TCRDock.TCRDock method) calculate_docking_geometry() (stcrpy.tcr_processing.TCR.TCR method) calculate_rmsd() (stcrpy.tcr_metrics.tcr_rmsd.RMSD method) calculate_rudolph_angle() (stcrpy.tcr_geometry.TCRGeom.TCRGeom method) calculate_tcr_docking_angles() (stcrpy.tcr_geometry.TCRGeom.TCRGeom method) call_anarci() (in module stcrpy.tcr_processing.annotate)

CD1 (class in stcrpy.tcr_processing.MHC) cdr3 (class in stcrpy.tcr_processing.Select) center_of_mass() (stcrpy.tcr_geometry.TCRCoM.TCRCoM method) check_residue_mapping() (stcrpy.tcr_metrics.tcr_interface_rmsd.InterfaceRMSD method) cleanup_scTCR_numbering() (in module stcrpy.tcr_processing.annotate) copy() (stcrpy.tcr_processing.Entity.Entity method) create_pymol_session() (stcrpy.tcr_interactions.TCRInteractionProfiler.TCRInteractionProfiler method)

D

dbTCR (class in stcrpy.tcr_processing.TCR)

DockingGeometryFilter (class in stcrpy.tcr_geometry.TCRGeomFiltering) DockingGeometryPDF (class in stcrpy.tcr_geometry.TCRGeomFiltering)

E

easy_alignment() (in module stcrpy.tcr_processing.annotate) Entity (class in stcrpy.tcr_processing.Entity)

ErrorStream (class in stcrpy.utils.error_stream) exclude_positions() (stcrpy.tcr_processing.utils.region_definitions.Accept method) extract_sequence() (in module stcrpy.tcr_processing.annotate)

F

fastcross() (in module stcrpy.tcr_processing.utils.common) fastnorm() (in module stcrpy.tcr_processing.utils.common) fetch_TCR() (in module stcrpy.tcr_methods.tcr_methods) fit() (stcrpy.tcr_geometry.TCRGeomFiltering.DockingGeometryPDF method) (stcrpy.tcr_geometry.TCRGeomFiltering.GammaPDF method) (stcrpy.tcr_geometry.TCRGeomFiltering.GaussianMixturePDF method)

Fragment (class in stcrpy.tcr_processing.Fragment) full_analysis() (stcrpy.tcr_methods.tcr_batch_operations.TCRBatchOperator method) fv_only_backbone (class in stcrpy.tcr_processing.Select)

G

GammaPDF (class in stcrpy.tcr_geometry.TCRGeomFiltering) GaussianMixturePDF (class in stcrpy.tcr_geometry.TCRGeomFiltering) gdTCR (class in stcrpy.tcr_processing.TCR) get() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphDataset method) get_alignment_dict() (in module stcrpy.tcr_processing.annotate) get_allele_assignments() (stcrpy.tcr_processing.MHC.MHC method) (stcrpy.tcr_processing.MHCchain.MHCchain method) get_alpha() (stcrpy.tcr_processing.MHC.MH1 method) (stcrpy.tcr_processing.MHC.scMH1 method) get_antigen() (stcrpy.tcr_processing.MHC.MHC method) (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRchain.TCRchain method) get_antigens() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_atoms() (stcrpy.tcr_processing.Fragment.Fragment method) (stcrpy.tcr_processing.MHC.MHC method) (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_B2M() (stcrpy.tcr_processing.MHC.CD1 method) (stcrpy.tcr_processing.MHC.MH1 method) (stcrpy.tcr_processing.MHC.MR1 method) (stcrpy.tcr_processing.MHC.scCD1 method) (stcrpy.tcr_processing.MHC.scMH1 method) get_CD1() (stcrpy.tcr_processing.MHC.CD1 method) (stcrpy.tcr_processing.MHC.scCD1 method) get_CDRs() (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRchain.TCRchain method) get_chains() (stcrpy.tcr_processing.MHC.MHC method) (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_chemical_name() (in module stcrpy.tcr_processing.Chemical_components) get_domain_assignment() (stcrpy.tcr_processing.TCR.abTCR method) (stcrpy.tcr_processing.TCR.dbTCR method) (stcrpy.tcr_processing.TCR.gdTCR method) get_filtered_MHC_residues() (stcrpy.tcr_geometry.TCRCoM.MHCI_TCRCoM method) (stcrpy.tcr_geometry.TCRCoM.MHCII_TCRCoM method) get_filtered_TCR_residues() (stcrpy.tcr_geometry.TCRCoM.TCRCoM method) get_fragments() (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCR.abTCR method) (stcrpy.tcr_processing.TCR.dbTCR method) (stcrpy.tcr_processing.TCR.gdTCR method) (stcrpy.tcr_processing.TCRchain.TCRchain method) get_frameworks() (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRchain.TCRchain method) get_from_expo() (in module stcrpy.tcr_processing.Chemical_components) get_GA() (stcrpy.tcr_processing.MHC.MH2 method) (stcrpy.tcr_processing.MHC.scMH2 method) get_GA1() (stcrpy.tcr_processing.MHC.MH1 method) (stcrpy.tcr_processing.MHC.scMH1 method) get_GA1L() (stcrpy.tcr_processing.MHC.scCD1 method) get_GA2() (stcrpy.tcr_processing.MHC.MH1 method) (stcrpy.tcr_processing.MHC.scMH1 method) get_GB() (stcrpy.tcr_processing.MHC.MH2 method) (stcrpy.tcr_processing.MHC.scMH2 method) get_germline_assignments() (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRchain.TCRchain method)

get_germlines_and_alleles() (in module stcrpy.tcr_methods.tcr_batch_operations) (stcrpy.tcr_methods.tcr_batch_operations.TCRBatchOperator method) (stcrpy.tcr_processing.TCR.TCR method) get_haddock_scores() (stcrpy.tcr_formats.tcr_haddock.HADDOCKResultsParser method) get_header() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_holders() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_interaction_heatmap() (stcrpy.tcr_interactions.TCRInteractionProfiler.TCRInteractionProfiler method) (stcrpy.tcr_processing.TCR.TCR method) get_interactions() (stcrpy.tcr_interactions.TCRInteractionProfiler.TCRInteractionProfiler method) get_interface_residues() (stcrpy.tcr_metrics.tcr_interface_rmsd.InterfaceRMSD method) get_interface_rmsd() (stcrpy.tcr_metrics.tcr_interface_rmsd.InterfaceRMSD method) get_MH1() (stcrpy.tcr_processing.MHC.MH1 method) (stcrpy.tcr_processing.MHC.scMH1 method) get_MHC() (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRchain.TCRchain method) get_MHC_allele_assignments() (stcrpy.tcr_processing.TCR.TCR method) get_MHC_type() (stcrpy.tcr_processing.MHC.MHC method) get_MHCs() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_models() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_MR1() (stcrpy.tcr_processing.MHC.MR1 method) get_name_type() (in module stcrpy.tcr_processing.Chemical_components) get_pitch_angle() (stcrpy.tcr_geometry.TCRGeom.TCRGeom method) (stcrpy.tcr_processing.TCR.TCR method) get_polarity() (stcrpy.tcr_geometry.TCRGeom.TCRGeom method) get_region() (in module stcrpy.tcr_processing.utils.region_definitions) get_res_type() (in module stcrpy.tcr_processing.Chemical_components) get_residues() (stcrpy.tcr_processing.Fragment.Fragment method) (stcrpy.tcr_processing.MHC.MHC method) (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_scanning_angle() (stcrpy.tcr_geometry.TCRGeom.TCRGeom method) (stcrpy.tcr_processing.TCR.TCR method) get_seq() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_sequence() (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCRchain.TCRchain method) get_sequences() (in module stcrpy.tcr_formats.tcr_formats) get_TCR() (stcrpy.tcr_processing.MHC.MHC method) (stcrpy.tcr_processing.MHCchain.MHCchain method) get_TCR_geometry() (in module stcrpy.tcr_methods.tcr_batch_operations) (stcrpy.tcr_methods.tcr_batch_operations.TCRBatchOperator method) get_TCR_interactions() (in module stcrpy.tcr_methods.tcr_batch_operations) get_TCR_pMHC_interactions() (stcrpy.tcr_methods.tcr_batch_operations.TCRBatchOperator method) get_tcr_structure() (stcrpy.tcr_processing.TCRParser.TCRParser method) get_TCR_type() (stcrpy.tcr_processing.TCR.TCR method) get_tcr_vector() (stcrpy.tcr_geometry.TCRGeom.TCRGeom method) get_TCRchains() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_TCRs() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_type() (stcrpy.tcr_processing.AGchain.AGchain method) get_unnumbered() (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCRchain.TCRchain method) get_unpaired_TCRchains() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) get_VA() (stcrpy.tcr_processing.TCR.abTCR method) get_VB() (stcrpy.tcr_processing.TCR.abTCR method) (stcrpy.tcr_processing.TCR.dbTCR method) get_VD() (stcrpy.tcr_processing.TCR.dbTCR method) (stcrpy.tcr_processing.TCR.gdTCR method) get_VG() (stcrpy.tcr_processing.TCR.gdTCR method)

H

HADDOCKFormatter (class in stcrpy.tcr_formats.tcr_haddock)

HADDOCKResultsParser (class in stcrpy.tcr_formats.tcr_haddock) Holder (class in stcrpy.tcr_processing.Holder)

I

identity() (in module stcrpy.tcr_processing.utils.common) imgt_insertion_char_to_int() (in module stcrpy.tcr_formats.tcr_haddock) insert() (stcrpy.tcr_processing.Fragment.Fragment method) Interaction (class in stcrpy.tcr_interactions.utils) InterfaceRMSD (class in stcrpy.tcr_metrics.tcr_interface_rmsd) interpret() (in module stcrpy.tcr_processing.annotate) is_aa() (in module stcrpy.tcr_processing.Chemical_components) is_bound() (stcrpy.tcr_processing.MHC.MHC method) (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRchain.TCRchain method)

is_carbohydrate() (in module stcrpy.tcr_processing.Chemical_components) is_common_buffer() (in module stcrpy.tcr_processing.Chemical_components) is_complete() (in module stcrpy.tcr_processing.Chemical_components) is_engineered() (stcrpy.tcr_processing.AGchain.AGchain method) (stcrpy.tcr_processing.TCR.abTCR method) (stcrpy.tcr_processing.TCR.dbTCR method) (stcrpy.tcr_processing.TCR.gdTCR method) (stcrpy.tcr_processing.TCRchain.TCRchain method) is_nucleic_acid() (in module stcrpy.tcr_processing.Chemical_components) is_polymer() (in module stcrpy.tcr_processing.Chemical_components)

L

len() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphDataset method) load_TCR() (in module stcrpy.tcr_methods.tcr_methods)

load_TCRs() (in module stcrpy.tcr_methods.tcr_methods) log_probs() (stcrpy.tcr_geometry.TCRGeomFiltering.DockingGeometryPDF method)

M

map_amino_acids_to_ligands() (stcrpy.tcr_interactions.TCRpMHC_PLIP_Model_Parser.TCRpMHC_PLIP_Model_Parser method) map_state_index_imgt() (in module stcrpy.tcr_processing.utils.region_definitions) map_state_index_mhc_clike() (in module stcrpy.tcr_processing.utils.region_definitions) MH1 (class in stcrpy.tcr_processing.MHC) MH2 (class in stcrpy.tcr_processing.MHC) MHC (class in stcrpy.tcr_processing.MHC) MHCchain (class in stcrpy.tcr_processing.MHCchain) MHCI_TCRCoM (class in stcrpy.tcr_geometry.TCRCoM) MHCII_TCRCoM (class in stcrpy.tcr_geometry.TCRCoM) Model (class in stcrpy.tcr_processing.Model) module stcrpy stcrpy.tcr_datasets stcrpy.tcr_datasets.tcr_graph_dataset stcrpy.tcr_datasets.tcr_selector stcrpy.tcr_datasets.tcr_structure_dataset stcrpy.tcr_datasets.utils stcrpy.tcr_formats stcrpy.tcr_formats.tcr_formats stcrpy.tcr_formats.tcr_haddock stcrpy.tcr_geometry stcrpy.tcr_geometry.reference_data stcrpy.tcr_geometry.reference_data.reference_data stcrpy.tcr_geometry.TCRCoM stcrpy.tcr_geometry.TCRDock stcrpy.tcr_geometry.TCRGeom stcrpy.tcr_geometry.TCRGeomFiltering stcrpy.tcr_interactions stcrpy.tcr_interactions.PLIPParser stcrpy.tcr_interactions.TCRInteractionProfiler stcrpy.tcr_interactions.TCRpMHC_PLIP_Model_Parser stcrpy.tcr_interactions.utils stcrpy.tcr_methods stcrpy.tcr_methods.tcr_batch_operations stcrpy.tcr_methods.tcr_methods stcrpy.tcr_methods.tcr_reformatting stcrpy.tcr_metrics stcrpy.tcr_metrics.constants stcrpy.tcr_metrics.tcr_interface_rmsd stcrpy.tcr_metrics.tcr_rmsd stcrpy.tcr_ml stcrpy.tcr_ml.geometry_predictor stcrpy.tcr_processing stcrpy.tcr_processing.AGchain stcrpy.tcr_processing.annotate stcrpy.tcr_processing.Chemical_components stcrpy.tcr_processing.Entity stcrpy.tcr_processing.Fragment stcrpy.tcr_processing.Holder stcrpy.tcr_processing.MHC stcrpy.tcr_processing.MHCchain stcrpy.tcr_processing.Model stcrpy.tcr_processing.Select stcrpy.tcr_processing.TCR stcrpy.tcr_processing.TCRchain stcrpy.tcr_processing.TCRIO stcrpy.tcr_processing.TCRParser stcrpy.tcr_processing.TCRStructure stcrpy.tcr_processing.utils stcrpy.tcr_processing.utils.common stcrpy.tcr_processing.utils.constants stcrpy.tcr_processing.utils.region_definitions stcrpy.utils stcrpy.utils.error_stream

MR1 (class in stcrpy.tcr_processing.MHC)

P

pairwise_alignment() (in module stcrpy.tcr_processing.annotate) parse_complex() (stcrpy.tcr_interactions.PLIPParser.PLIPParser method) parse_interaction() (in module stcrpy.tcr_interactions.utils) parse_renumbered_line() (in module stcrpy.tcr_formats.tcr_haddock) parse_tcr_pmhc_complex() (stcrpy.tcr_interactions.TCRpMHC_PLIP_Model_Parser.TCRpMHC_PLIP_Model_Parser method) pdf() (stcrpy.tcr_geometry.TCRGeomFiltering.DockingGeometryPDF method) (stcrpy.tcr_geometry.TCRGeomFiltering.GammaPDF method) (stcrpy.tcr_geometry.TCRGeomFiltering.GaussianMixturePDF method) PitchAnglePDF (class in stcrpy.tcr_geometry.TCRGeomFiltering) PLIPParser (class in stcrpy.tcr_interactions.PLIPParser) plot() (stcrpy.tcr_geometry.TCRGeomFiltering.DockingGeometryPDF method)

pMHC_to_haddock() (stcrpy.tcr_formats.tcr_haddock.HADDOCKFormatter method) pop() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphDataset method) process() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphDataset method) process_hbond() (in module stcrpy.tcr_interactions.utils) process_hydrophobic() (in module stcrpy.tcr_interactions.utils) process_pi_stack() (in module stcrpy.tcr_interactions.utils) process_saltbridge() (in module stcrpy.tcr_interactions.utils) processed_file_names (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphDataset property) profile_MHC_interactions() (stcrpy.tcr_processing.TCR.TCR method) profile_peptide_interactions() (stcrpy.tcr_processing.TCR.TCR method) profile_TCR_interactions() (stcrpy.tcr_processing.TCR.TCR method)

R

raw_file_names (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphDataset property) renumber_all_haddock_predictions() (stcrpy.tcr_formats.tcr_haddock.HADDOCKResultsParser method) renumber_haddock_prediction() (stcrpy.tcr_formats.tcr_haddock.HADDOCKResultsParser method)

reset_parameters() (stcrpy.tcr_interactions.TCRInteractionProfiler.TCRInteractionProfiler method) return_interactions() (in module stcrpy.tcr_interactions.utils) RMSD (class in stcrpy.tcr_metrics.tcr_rmsd) rmsd_from_files() (stcrpy.tcr_metrics.tcr_rmsd.RMSD method)

S

save() (stcrpy.tcr_processing.Entity.Entity method) (stcrpy.tcr_processing.TCR.TCR method) (stcrpy.tcr_processing.TCRIO.TCRIO method) ScanningAnglePDF (class in stcrpy.tcr_geometry.TCRGeomFiltering) scCD1 (class in stcrpy.tcr_processing.MHC) scMH1 (class in stcrpy.tcr_processing.MHC) scMH2 (class in stcrpy.tcr_processing.MHC) score_docking_geometry() (stcrpy.tcr_geometry.TCRGeomFiltering.DockingGeometryFilter method) (stcrpy.tcr_processing.TCR.TCR method) select_all (class in stcrpy.tcr_processing.Select) set_chain_type() (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCRchain.TCRchain method) set_edge_featuriser() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphConstructor method) set_engineered() (stcrpy.tcr_processing.AGchain.AGchain method) (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCRchain.TCRchain method) set_header() (stcrpy.tcr_processing.TCRStructure.TCRStructure method) set_interaction_parameters() (stcrpy.tcr_interactions.TCRInteractionProfiler.TCRInteractionProfiler method) set_mhc_reference() (stcrpy.tcr_geometry.TCRCoM.MHCI_TCRCoM method) (stcrpy.tcr_geometry.TCRCoM.MHCII_TCRCoM method) (stcrpy.tcr_geometry.TCRCoM.TCRCoM method) set_node_featuriser() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphConstructor method) set_node_selector() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphConstructor method) set_pitch_angle_pdf() (stcrpy.tcr_geometry.TCRGeomFiltering.DockingGeometryFilter method) set_reference_residues() (stcrpy.tcr_geometry.TCRCoM.TCRCoM method) set_reffile() (stcrpy.tcr_geometry.TCRCoM.MHCI_TCRCoM method) (stcrpy.tcr_geometry.TCRCoM.MHCII_TCRCoM method) (stcrpy.tcr_geometry.TCRCoM.TCRCoM method) set_regions() (stcrpy.tcr_processing.utils.region_definitions.Accept method) set_scanning_angle_pdf() (stcrpy.tcr_geometry.TCRGeomFiltering.DockingGeometryFilter method) set_sequence() (stcrpy.tcr_processing.MHCchain.MHCchain method) (stcrpy.tcr_processing.TCRchain.TCRchain method) set_tcr_reference() (stcrpy.tcr_geometry.TCRCoM.TCRCoM method) set_type() (stcrpy.tcr_processing.AGchain.AGchain method) set_y() (stcrpy.tcr_datasets.tcr_graph_dataset.TCRGraphDataset method) set_zdist_angle_pdf() (stcrpy.tcr_geometry.TCRGeomFiltering.DockingGeometryFilter method) sort_residues_by_imgt_numbering() (in module stcrpy.tcr_formats.tcr_haddock) stcrpy module stcrpy.tcr_datasets module stcrpy.tcr_datasets.tcr_graph_dataset module stcrpy.tcr_datasets.tcr_selector module stcrpy.tcr_datasets.tcr_structure_dataset module stcrpy.tcr_datasets.utils module stcrpy.tcr_formats module stcrpy.tcr_formats.tcr_formats module stcrpy.tcr_formats.tcr_haddock module stcrpy.tcr_geometry module stcrpy.tcr_geometry.reference_data module stcrpy.tcr_geometry.reference_data.reference_data module stcrpy.tcr_geometry.TCRCoM module stcrpy.tcr_geometry.TCRDock module stcrpy.tcr_geometry.TCRGeom module stcrpy.tcr_geometry.TCRGeomFiltering module stcrpy.tcr_interactions module

stcrpy.tcr_interactions.PLIPParser module stcrpy.tcr_interactions.TCRInteractionProfiler module stcrpy.tcr_interactions.TCRpMHC_PLIP_Model_Parser module stcrpy.tcr_interactions.utils module stcrpy.tcr_methods module stcrpy.tcr_methods.tcr_batch_operations module stcrpy.tcr_methods.tcr_methods module stcrpy.tcr_methods.tcr_reformatting module stcrpy.tcr_metrics module stcrpy.tcr_metrics.constants module stcrpy.tcr_metrics.tcr_interface_rmsd module stcrpy.tcr_metrics.tcr_rmsd module stcrpy.tcr_ml module stcrpy.tcr_ml.geometry_predictor module stcrpy.tcr_processing module stcrpy.tcr_processing.AGchain module stcrpy.tcr_processing.annotate module stcrpy.tcr_processing.Chemical_components module stcrpy.tcr_processing.Entity module stcrpy.tcr_processing.Fragment module stcrpy.tcr_processing.Holder module stcrpy.tcr_processing.MHC module stcrpy.tcr_processing.MHCchain module stcrpy.tcr_processing.Model module stcrpy.tcr_processing.Select module stcrpy.tcr_processing.TCR module stcrpy.tcr_processing.TCRchain module stcrpy.tcr_processing.TCRIO module stcrpy.tcr_processing.TCRParser module stcrpy.tcr_processing.TCRStructure module stcrpy.tcr_processing.utils module stcrpy.tcr_processing.utils.common module stcrpy.tcr_processing.utils.constants module stcrpy.tcr_processing.utils.region_definitions module stcrpy.utils module stcrpy.utils.error_stream module

T

TCR (class in stcrpy.tcr_processing.TCR) tcr_to_haddock() (stcrpy.tcr_formats.tcr_haddock.HADDOCKFormatter method) TCRBatchOperator (class in stcrpy.tcr_methods.tcr_batch_operations) TCRchain (class in stcrpy.tcr_processing.TCRchain) TCRCoM (class in stcrpy.tcr_geometry.TCRCoM) TCRDock (class in stcrpy.tcr_geometry.TCRDock) TCRGeom (class in stcrpy.tcr_geometry.TCRGeom) TCRGraphConstructor (class in stcrpy.tcr_datasets.tcr_graph_dataset) TCRGraphDataset (class in stcrpy.tcr_datasets.tcr_graph_dataset) TCRInteractionProfiler (class in stcrpy.tcr_interactions.TCRInteractionProfiler) TCRIO (class in stcrpy.tcr_processing.TCRIO)

TCRParser (class in stcrpy.tcr_processing.TCRParser) TCRpMHC_PLIP_Model_Parser (class in stcrpy.tcr_interactions.TCRpMHC_PLIP_Model_Parser) tcrs_from_file_dict() (stcrpy.tcr_methods.tcr_batch_operations.TCRBatchOperator method) tcrs_from_file_list() (stcrpy.tcr_methods.tcr_batch_operations.TCRBatchOperator method) tcrs_to_AF3_json() (in module stcrpy.tcr_methods.tcr_reformatting) TCRStructure (class in stcrpy.tcr_processing.TCRStructure) to_AF3_json() (in module stcrpy.tcr_formats.tcr_formats) to_df() (stcrpy.tcr_geometry.TCRGeom.TCRGeom method) to_dict() (stcrpy.tcr_geometry.TCRGeom.TCRGeom method) to_tuple() (stcrpy.tcr_interactions.utils.Interaction method) transform() (stcrpy.tcr_processing.Entity.Entity method) tuplefy() (in module stcrpy.tcr_processing.utils.constants)

V

validate_sequence() (in module stcrpy.tcr_processing.annotate)

variable_only (class in stcrpy.tcr_processing.Select)

W

write() (stcrpy.utils.error_stream.ErrorStream method)

write_antigen_pdb_file() (stcrpy.tcr_formats.tcr_haddock.HADDOCKFormatter method) write_TCR_pdb_file() (stcrpy.tcr_formats.tcr_haddock.HADDOCKFormatter method)

Y

yield_TCRs() (in module stcrpy.tcr_methods.tcr_methods)

Z

ZDistPDF (class in stcrpy.tcr_geometry.TCRGeomFiltering)