stcrpy package

Subpackages

• stcrpy.tcr_datasets package
  • Submodules
  • stcrpy.tcr_datasets.tcr_graph_dataset module
    • TCRGraphConstructor
      • TCRGraphConstructor.build_graph()
      • TCRGraphConstructor.set_edge_featuriser()
      • TCRGraphConstructor.set_node_featuriser()
      • TCRGraphConstructor.set_node_selector()
    • TCRGraphDataset
      • TCRGraphDataset.get()
      • TCRGraphDataset.len()
      • TCRGraphDataset.pop()
      • TCRGraphDataset.process()
      • TCRGraphDataset.processed_file_names
      • TCRGraphDataset.raw_file_names
      • TCRGraphDataset.set_y()
  • stcrpy.tcr_datasets.tcr_selector module
  • stcrpy.tcr_datasets.tcr_structure_dataset module
  • stcrpy.tcr_datasets.utils module
  • Module contents
• stcrpy.tcr_formats package
  • Submodules
  • stcrpy.tcr_formats.tcr_formats module
    • get_sequences()
    • to_AF3_json()
  • stcrpy.tcr_formats.tcr_haddock module
    • HADDOCKFormatter
      • HADDOCKFormatter.pMHC_to_haddock()
      • HADDOCKFormatter.tcr_to_haddock()
      • HADDOCKFormatter.write_TCR_pdb_file()
      • HADDOCKFormatter.write_antigen_pdb_file()
    • HADDOCKResultsParser
      • HADDOCKResultsParser.get_haddock_scores()
      • HADDOCKResultsParser.renumber_all_haddock_predictions()
      • HADDOCKResultsParser.renumber_haddock_prediction()
    • imgt_insertion_char_to_int()
    • parse_renumbered_line()
    • sort_residues_by_imgt_numbering()
  • Module contents
• stcrpy.tcr_geometry package
  • Subpackages
    • stcrpy.tcr_geometry.reference_data package
      • Submodules
      • stcrpy.tcr_geometry.reference_data.reference_data module
      • Module contents
  • Submodules
  • stcrpy.tcr_geometry.TCRCoM module
    • MHCII_TCRCoM
      • MHCII_TCRCoM.get_filtered_MHC_residues()
      • MHCII_TCRCoM.set_mhc_reference()
      • MHCII_TCRCoM.set_reffile()
    • MHCI_TCRCoM
      • MHCI_TCRCoM.get_filtered_MHC_residues()
      • MHCI_TCRCoM.set_mhc_reference()
      • MHCI_TCRCoM.set_reffile()
    • TCRCoM
      • TCRCoM.add_com()
      • TCRCoM.calculate_centres_of_mass()
      • TCRCoM.center_of_mass()
      • TCRCoM.get_filtered_TCR_residues()
      • TCRCoM.set_mhc_reference()
      • TCRCoM.set_reference_residues()
      • TCRCoM.set_reffile()
      • TCRCoM.set_tcr_reference()
  • stcrpy.tcr_geometry.TCRDock module
    • TCRDock
      • TCRDock.calculate_docking_angle()
  • stcrpy.tcr_geometry.TCRGeom module
    • TCRGeom
      • TCRGeom.calculate_rudolph_angle()
      • TCRGeom.calculate_tcr_docking_angles()
      • TCRGeom.get_pitch_angle()
      • TCRGeom.get_polarity()
      • TCRGeom.get_scanning_angle()
      • TCRGeom.get_tcr_vector()
      • TCRGeom.to_df()
      • TCRGeom.to_dict()
  • stcrpy.tcr_geometry.TCRGeomFiltering module
    • DockingGeometryFilter
      • DockingGeometryFilter.score_docking_geometry()
      • DockingGeometryFilter.set_pitch_angle_pdf()
      • DockingGeometryFilter.set_scanning_angle_pdf()
      • DockingGeometryFilter.set_zdist_angle_pdf()
    • DockingGeometryPDF
      • DockingGeometryPDF.fit()
      • DockingGeometryPDF.log_probs()
      • DockingGeometryPDF.pdf()
      • DockingGeometryPDF.plot()
    • GammaPDF
      • GammaPDF.fit()
      • GammaPDF.pdf()
    • GaussianMixturePDF
      • GaussianMixturePDF.fit()
      • GaussianMixturePDF.pdf()
    • PitchAnglePDF
    • ScanningAnglePDF
    • ZDistPDF
  • Module contents
• stcrpy.tcr_interactions package
  • Submodules
  • stcrpy.tcr_interactions.PLIPParser module
    • PLIPParser
      • PLIPParser.parse_complex()
  • stcrpy.tcr_interactions.TCRInteractionProfiler module
    • TCRInteractionProfiler
      • TCRInteractionProfiler.create_pymol_session()
      • TCRInteractionProfiler.get_interaction_heatmap()
      • TCRInteractionProfiler.get_interactions()
      • TCRInteractionProfiler.reset_parameters()
      • TCRInteractionProfiler.set_interaction_parameters()
  • stcrpy.tcr_interactions.TCRpMHC_PLIP_Model_Parser module
    • TCRpMHC_PLIP_Model_Parser
      • TCRpMHC_PLIP_Model_Parser.map_amino_acids_to_ligands()
      • TCRpMHC_PLIP_Model_Parser.parse_tcr_pmhc_complex()
  • stcrpy.tcr_interactions.utils module
    • Interaction
      • Interaction.to_tuple()
    • parse_interaction()
    • process_hbond()
    • process_hydrophobic()
    • process_pi_stack()
    • process_saltbridge()
    • return_interactions()
  • Module contents
• stcrpy.tcr_methods package
  • Submodules
  • stcrpy.tcr_methods.tcr_batch_operations module
    • TCRBatchOperator
      • TCRBatchOperator.full_analysis()
      • TCRBatchOperator.get_TCR_geometry()
      • TCRBatchOperator.get_TCR_pMHC_interactions()
      • TCRBatchOperator.get_germlines_and_alleles()
      • TCRBatchOperator.tcrs_from_file_dict()
      • TCRBatchOperator.tcrs_from_file_list()
    • analyse_tcrs()
    • batch_load_TCRs()
    • batch_yield_TCRs()
    • get_TCR_geometry()
    • get_TCR_interactions()
    • get_germlines_and_alleles()
  • stcrpy.tcr_methods.tcr_methods module
    • fetch_TCR()
    • load_TCR()
    • load_TCRs()
    • yield_TCRs()
  • stcrpy.tcr_methods.tcr_reformatting module
    • tcrs_to_AF3_json()
  • Module contents
• stcrpy.tcr_metrics package
  • Submodules
  • stcrpy.tcr_metrics.constants module
  • stcrpy.tcr_metrics.tcr_interface_rmsd module
    • InterfaceRMSD
      • InterfaceRMSD.align_by_mhc()
      • InterfaceRMSD.check_residue_mapping()
      • InterfaceRMSD.get_interface_residues()
      • InterfaceRMSD.get_interface_rmsd()
  • stcrpy.tcr_metrics.tcr_rmsd module
    • RMSD
      • RMSD.calculate_rmsd()
      • RMSD.rmsd_from_files()
  • Module contents
• stcrpy.tcr_ml package
  • Submodules
  • stcrpy.tcr_ml.geometry_predictor module
  • Module contents
• stcrpy.tcr_processing package
  • Subpackages
    • stcrpy.tcr_processing.utils package
      • Submodules
      • stcrpy.tcr_processing.utils.common module
      • stcrpy.tcr_processing.utils.constants module
      • stcrpy.tcr_processing.utils.region_definitions module
      • Module contents
  • Submodules
  • stcrpy.tcr_processing.AGchain module
    • AGchain
      • AGchain.get_type()
      • AGchain.is_engineered()
      • AGchain.set_engineered()
      • AGchain.set_type()
  • stcrpy.tcr_processing.Chemical_components module
    • get_chemical_name()
    • get_from_expo()
    • get_name_type()
    • get_res_type()
    • is_aa()
    • is_carbohydrate()
    • is_common_buffer()
    • is_complete()
    • is_nucleic_acid()
    • is_polymer()
  • stcrpy.tcr_processing.Entity module
    • Entity
      • Entity.copy()
      • Entity.save()
      • Entity.transform()
  • stcrpy.tcr_processing.Fragment module
    • Fragment
      • Fragment.add()
      • Fragment.get_atoms()
      • Fragment.get_residues()
      • Fragment.insert()
  • stcrpy.tcr_processing.Holder module
    • Holder
  • stcrpy.tcr_processing.MHC module
    • CD1
      • CD1.get_B2M()
      • CD1.get_CD1()
    • MH1
      • MH1.get_B2M()
      • MH1.get_GA1()
      • MH1.get_GA2()
      • MH1.get_MH1()
      • MH1.get_alpha()
    • MH2
      • MH2.get_GA()
      • MH2.get_GB()
    • MHC
      • MHC.get_MHC_type()
      • MHC.get_TCR()
      • MHC.get_allele_assignments()
      • MHC.get_antigen()
      • MHC.get_atoms()
      • MHC.get_chains()
      • MHC.get_residues()
      • MHC.is_bound()
    • MR1
      • MR1.get_B2M()
      • MR1.get_MR1()
    • scCD1
      • scCD1.get_B2M()
      • scCD1.get_CD1()
      • scCD1.get_GA1L()
    • scMH1
      • scMH1.get_B2M()
      • scMH1.get_GA1()
      • scMH1.get_GA2()
      • scMH1.get_MH1()
      • scMH1.get_alpha()
    • scMH2
      • scMH2.get_GA()
      • scMH2.get_GB()
  • stcrpy.tcr_processing.MHCchain module
    • MHCchain
      • MHCchain.add_unnumbered()
      • MHCchain.analyse()
      • MHCchain.annotate_children()
      • MHCchain.get_TCR()
      • MHCchain.get_allele_assignments()
      • MHCchain.get_antigen()
      • MHCchain.get_chains()
      • MHCchain.get_fragments()
      • MHCchain.get_sequence()
      • MHCchain.get_unnumbered()
      • MHCchain.is_bound()
      • MHCchain.set_chain_type()
      • MHCchain.set_engineered()
      • MHCchain.set_sequence()
  • stcrpy.tcr_processing.Model module
    • Model
  • stcrpy.tcr_processing.Select module
    • backbone
      • backbone.accept_atom()
    • cdr3
      • cdr3.accept_residue()
    • fv_only_backbone
    • select_all
      • select_all.accept()
      • select_all.accept_atom()
      • select_all.accept_chain()
      • select_all.accept_fragment()
      • select_all.accept_holder()
      • select_all.accept_model()
      • select_all.accept_residue()
    • variable_only
      • variable_only.accept_holder()
      • variable_only.accept_residue()
  • stcrpy.tcr_processing.TCR module
    • TCR
      • TCR.calculate_docking_geometry()
      • TCR.get_CDRs()
      • TCR.get_MHC()
      • TCR.get_MHC_allele_assignments()
      • TCR.get_TCR_type()
      • TCR.get_antigen()
      • TCR.get_atoms()
      • TCR.get_chains()
      • TCR.get_frameworks()
      • TCR.get_germline_assignments()
      • TCR.get_germlines_and_alleles()
      • TCR.get_interaction_heatmap()
      • TCR.get_pitch_angle()
      • TCR.get_residues()
      • TCR.get_scanning_angle()
      • TCR.is_bound()
      • TCR.profile_MHC_interactions()
      • TCR.profile_TCR_interactions()
      • TCR.profile_peptide_interactions()
      • TCR.save()
      • TCR.score_docking_geometry()
    • abTCR
      • abTCR.get_VA()
      • abTCR.get_VB()
      • abTCR.get_domain_assignment()
      • abTCR.get_fragments()
      • abTCR.is_engineered()
    • dbTCR
      • dbTCR.get_VB()
      • dbTCR.get_VD()
      • dbTCR.get_domain_assignment()
      • dbTCR.get_fragments()
      • dbTCR.is_engineered()
    • gdTCR
      • gdTCR.get_VD()
      • gdTCR.get_VG()
      • gdTCR.get_domain_assignment()
      • gdTCR.get_fragments()
      • gdTCR.is_engineered()
  • stcrpy.tcr_processing.TCRIO module
    • TCRIO
      • TCRIO.save()
  • stcrpy.tcr_processing.TCRParser module
    • TCRParser
      • TCRParser.get_tcr_structure()
  • stcrpy.tcr_processing.TCRStructure module
    • TCRStructure
      • TCRStructure.get_MHCs()
      • TCRStructure.get_TCRchains()
      • TCRStructure.get_TCRs()
      • TCRStructure.get_antigens()
      • TCRStructure.get_atoms()
      • TCRStructure.get_chains()
      • TCRStructure.get_header()
      • TCRStructure.get_holders()
      • TCRStructure.get_models()
      • TCRStructure.get_residues()
      • TCRStructure.get_seq()
      • TCRStructure.get_unpaired_TCRchains()
      • TCRStructure.set_header()
  • stcrpy.tcr_processing.TCRchain module
    • TCRchain
      • TCRchain.add_unnumbered()
      • TCRchain.analyse()
      • TCRchain.annotate_children()
      • TCRchain.get_CDRs()
      • TCRchain.get_MHC()
      • TCRchain.get_antigen()
      • TCRchain.get_fragments()
      • TCRchain.get_frameworks()
      • TCRchain.get_germline_assignments()
      • TCRchain.get_sequence()
      • TCRchain.get_unnumbered()
      • TCRchain.is_bound()
      • TCRchain.is_engineered()
      • TCRchain.set_chain_type()
      • TCRchain.set_engineered()
      • TCRchain.set_sequence()
  • stcrpy.tcr_processing.annotate module
    • align_numbering()
    • align_scTCR_numbering()
    • annotate()
    • call_anarci()
    • cleanup_scTCR_numbering()
    • easy_alignment()
    • extract_sequence()
    • get_alignment_dict()
    • interpret()
    • pairwise_alignment()
    • validate_sequence()
  • Module contents
• stcrpy.utils package
  • Submodules
  • stcrpy.utils.error_stream module
    • ErrorStream
      • ErrorStream.write()
  • Module contents

Module contents