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MHCXGraph 0.1.1 documentation
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MHCXGraph 0.1.1 documentation

Python Package

  • Installation
  • Getting Started
  • Execution Configuration (Manifest)
  • Examples
  • API Reference
    • MHCXGraph
      • MHCXGraph.app
        • MHCXGraph.app.clean_graph_name
        • MHCXGraph.app.create_master_dashboard
        • MHCXGraph.app.main
        • MHCXGraph.app.renumber
        • MHCXGraph.app.run
        • MHCXGraph.app.run_multiple_mode
        • MHCXGraph.app.run_pairwise_mode
        • MHCXGraph.app.run_screening_mode
        • MHCXGraph.app.setup_trackers
      • MHCXGraph.classes
        • MHCXGraph.classes.graph
          • MHCXGraph.classes.graph.AssociatedGraph
          • MHCXGraph.classes.graph.Graph
          • MHCXGraph.classes.graph.GraphData
      • MHCXGraph.cli
        • MHCXGraph.cli.cli_parser
          • MHCXGraph.cli.cli_parser.none_or_float
          • MHCXGraph.cli.cli_parser.parse_args
          • MHCXGraph.cli.cli_parser.str2bool
      • MHCXGraph.core
        • MHCXGraph.core.config
          • MHCXGraph.core.config.DSSPConfig
          • MHCXGraph.core.config.GraphConfig
          • MHCXGraph.core.config.make_default_config
        • MHCXGraph.core.contact_map
          • MHCXGraph.core.contact_map.contact_map_from_graph
        • MHCXGraph.core.metadata
          • MHCXGraph.core.metadata.secondary_structure
        • MHCXGraph.core.pdb_graph_builder
          • MHCXGraph.core.pdb_graph_builder.AtomBundle
          • MHCXGraph.core.pdb_graph_builder.BuiltGraph
          • MHCXGraph.core.pdb_graph_builder.FixedPDBIO
          • MHCXGraph.core.pdb_graph_builder.NodeCoords
          • MHCXGraph.core.pdb_graph_builder.PDBGraphBuilder
          • MHCXGraph.core.pdb_graph_builder.ResidueInfo
          • MHCXGraph.core.pdb_graph_builder.StructureDict
          • MHCXGraph.core.pdb_graph_builder.capture_c_stderr
          • MHCXGraph.core.pdb_graph_builder.check_res_inconsistencies
        • MHCXGraph.core.pipeline
          • MHCXGraph.core.pipeline.build_graph_with_config
        • MHCXGraph.core.residue_tracking
          • MHCXGraph.core.residue_tracking.ResidueTracker
          • MHCXGraph.core.residue_tracking.TrackCtx
          • MHCXGraph.core.residue_tracking.combo_residues
          • MHCXGraph.core.residue_tracking.parse_node_label
          • MHCXGraph.core.residue_tracking.residue_key
          • MHCXGraph.core.residue_tracking.triad_residues_from_absolute
        • MHCXGraph.core.subgraphs
          • MHCXGraph.core.subgraphs.compute_distmat
          • MHCXGraph.core.subgraphs.extract_interface_subgraph
          • MHCXGraph.core.subgraphs.extract_k_hop_subgraph
          • MHCXGraph.core.subgraphs.extract_subgraph
          • MHCXGraph.core.subgraphs.extract_subgraph_by_bond_type
          • MHCXGraph.core.subgraphs.extract_subgraph_by_sequence_position
          • MHCXGraph.core.subgraphs.extract_subgraph_from_atom_types
          • MHCXGraph.core.subgraphs.extract_subgraph_from_chains
          • MHCXGraph.core.subgraphs.extract_subgraph_from_node_list
          • MHCXGraph.core.subgraphs.extract_subgraph_from_point
          • MHCXGraph.core.subgraphs.extract_subgraph_from_residue_types
          • MHCXGraph.core.subgraphs.extract_subgraph_from_secondary_structure
          • MHCXGraph.core.subgraphs.extract_surface_subgraph_asa
          • MHCXGraph.core.subgraphs.extract_surface_subgraph_rsa
          • MHCXGraph.core.subgraphs.ProteinGraphConfigurationError
        • MHCXGraph.core.tracking
          • MHCXGraph.core.tracking.Tracker
          • MHCXGraph.core.tracking.TrackerConfig
          • MHCXGraph.core.tracking.get_current
          • MHCXGraph.core.tracking.init_tracker
          • MHCXGraph.core.tracking.mark
          • MHCXGraph.core.tracking.save
          • MHCXGraph.core.tracking.set_enabled
          • MHCXGraph.core.tracking.track
          • MHCXGraph.core.tracking.tracked
      • MHCXGraph.io_utils
        • MHCXGraph.io_utils.pdb_io
          • MHCXGraph.io_utils.pdb_io.get_user_selection
          • MHCXGraph.io_utils.pdb_io.list_pdb_files
      • MHCXGraph.scripts
        • MHCXGraph.scripts.create_heatmaps
          • MHCXGraph.scripts.create_heatmaps.build_component_matrix
          • MHCXGraph.scripts.create_heatmaps.create_distance_matrix
          • MHCXGraph.scripts.create_heatmaps.create_heatmap
          • MHCXGraph.scripts.create_heatmaps.extract_original_graph_info
          • MHCXGraph.scripts.create_heatmaps.extract_unique_aminoacids
          • MHCXGraph.scripts.create_heatmaps.process_directories
        • MHCXGraph.scripts.renumber_MHCII_imgt
          • MHCXGraph.scripts.renumber_MHCII_imgt.align_query_to_template
          • MHCXGraph.scripts.renumber_MHCII_imgt.choose_best_template_for_chain
          • MHCXGraph.scripts.renumber_MHCII_imgt.compute_alignment_stats
          • MHCXGraph.scripts.renumber_MHCII_imgt.continue_numbering_from_unmatched
          • MHCXGraph.scripts.renumber_MHCII_imgt.detect_mhcII_chains
          • MHCXGraph.scripts.renumber_MHCII_imgt.get_chain_polymer_residues
          • MHCXGraph.scripts.renumber_MHCII_imgt.get_chain_sequence_and_residues
          • MHCXGraph.scripts.renumber_MHCII_imgt.load_mhcii_templates
          • MHCXGraph.scripts.renumber_MHCII_imgt.load_structure
          • MHCXGraph.scripts.renumber_MHCII_imgt.main
          • MHCXGraph.scripts.renumber_MHCII_imgt.parse_imgt_label
          • MHCXGraph.scripts.renumber_MHCII_imgt.print_alignment_blocks
          • MHCXGraph.scripts.renumber_MHCII_imgt.print_debug_alignment
          • MHCXGraph.scripts.renumber_MHCII_imgt.process_structure_file_mhcii
          • MHCXGraph.scripts.renumber_MHCII_imgt.project_query_onto_gapped_template
          • MHCXGraph.scripts.renumber_MHCII_imgt.renumber_chain_from_projection
          • MHCXGraph.scripts.renumber_MHCII_imgt.residue_to_one_letter
          • MHCXGraph.scripts.renumber_MHCII_imgt.save_structure
        • MHCXGraph.scripts.renumber_MHCI_imgt
          • MHCXGraph.scripts.renumber_MHCI_imgt.align_query_to_template
          • MHCXGraph.scripts.renumber_MHCI_imgt.choose_best_template_for_chain
          • MHCXGraph.scripts.renumber_MHCI_imgt.compute_alignment_stats
          • MHCXGraph.scripts.renumber_MHCI_imgt.continue_numbering_from_unmatched
          • MHCXGraph.scripts.renumber_MHCI_imgt.detect_mhci_chain
          • MHCXGraph.scripts.renumber_MHCI_imgt.get_chain_polymer_residues
          • MHCXGraph.scripts.renumber_MHCI_imgt.get_chain_sequence_and_residues
          • MHCXGraph.scripts.renumber_MHCI_imgt.load_mhci_templates
          • MHCXGraph.scripts.renumber_MHCI_imgt.load_structure
          • MHCXGraph.scripts.renumber_MHCI_imgt.main
          • MHCXGraph.scripts.renumber_MHCI_imgt.normalize_numbering_column
          • MHCXGraph.scripts.renumber_MHCI_imgt.parse_imgt_label
          • MHCXGraph.scripts.renumber_MHCI_imgt.print_alignment_blocks
          • MHCXGraph.scripts.renumber_MHCI_imgt.print_debug_alignment
          • MHCXGraph.scripts.renumber_MHCI_imgt.process_structure_file_mhci
          • MHCXGraph.scripts.renumber_MHCI_imgt.project_query_onto_gapped_template
          • MHCXGraph.scripts.renumber_MHCI_imgt.renumber_chain_from_projection
          • MHCXGraph.scripts.renumber_MHCI_imgt.residue_to_one_letter
          • MHCXGraph.scripts.renumber_MHCI_imgt.save_structure
      • MHCXGraph.utils
        • MHCXGraph.utils.analysis
          • MHCXGraph.utils.analysis.chain_signature
          • MHCXGraph.utils.analysis.evaluate_all_frames_nodes
          • MHCXGraph.utils.analysis.evaluate_all_frames_nodes_weighted
          • MHCXGraph.utils.analysis.evaluate_frame_nodes
          • MHCXGraph.utils.analysis.get_protein_keys
          • MHCXGraph.utils.analysis.ivw_mean_proportions
          • MHCXGraph.utils.analysis.node_similarity_for_protein
          • MHCXGraph.utils.analysis.project_nodes_instances
          • MHCXGraph.utils.analysis.summarize_frame_nodes
          • MHCXGraph.utils.analysis.unique_chain_signatures
          • MHCXGraph.utils.analysis.wmean
          • MHCXGraph.utils.analysis.wmedian
          • MHCXGraph.utils.analysis.wstd
          • MHCXGraph.utils.analysis.wtrimmed_mean
        • MHCXGraph.utils.logging_utils
          • MHCXGraph.utils.logging_utils.ConsoleFilter
          • MHCXGraph.utils.logging_utils.VerboseLoggerAdapter
          • MHCXGraph.utils.logging_utils.get_log
          • MHCXGraph.utils.logging_utils.setup_logging
        • MHCXGraph.utils.preprocessing
          • MHCXGraph.utils.preprocessing.collect_selected_files_from_manifest
          • MHCXGraph.utils.preprocessing.create_graphs
          • MHCXGraph.utils.preprocessing.get_exposed_residues
          • MHCXGraph.utils.preprocessing.list_struct_files
          • MHCXGraph.utils.preprocessing.resolve_selection_params_for_file
          • MHCXGraph.utils.preprocessing.LogicError
        • MHCXGraph.utils.pyvis_inject
          • MHCXGraph.utils.pyvis_inject.inject_fullscreen_css
          • MHCXGraph.utils.pyvis_inject.inject_std_hover
          • MHCXGraph.utils.pyvis_inject.load_pyvis_std_js
        • MHCXGraph.utils.tools
          • MHCXGraph.utils.tools.association_product
          • MHCXGraph.utils.tools.build_graph_from_cross_combos
          • MHCXGraph.utils.tools.build_threshold_vector
          • MHCXGraph.utils.tools.convert_edges_to_residues
          • MHCXGraph.utils.tools.create_coherent_matrices
          • MHCXGraph.utils.tools.create_graph
          • MHCXGraph.utils.tools.cross_protein_triads
          • MHCXGraph.utils.tools.execute_step
          • MHCXGraph.utils.tools.filter_maps_by_nodes
          • MHCXGraph.utils.tools.find_class
          • MHCXGraph.utils.tools.find_triads
          • MHCXGraph.utils.tools.generate_frames
          • MHCXGraph.utils.tools.get_memory_usage_mb
          • MHCXGraph.utils.tools.parse_node
          • MHCXGraph.utils.tools.process_chunk
          • MHCXGraph.utils.tools.rebuild_cross_combos
          • MHCXGraph.utils.tools.residue_to_tuple
          • MHCXGraph.utils.tools.sym_from_packed_bool
          • MHCXGraph.utils.tools.sym_from_packed_float
          • MHCXGraph.utils.tools.triad_chirality_with_cb
          • MHCXGraph.utils.tools.value_to_class
      • MHCXGraph.workflow
        • MHCXGraph.workflow.association
          • MHCXGraph.workflow.association.run_association_task
        • MHCXGraph.workflow.manifest
          • MHCXGraph.workflow.manifest.build_association_config
          • MHCXGraph.workflow.manifest.load_manifest
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MHCXGraph.core¶

Submodules¶

config

contact_map

metadata

pdb_graph_builder

pipeline

residue_tracking

subgraphs

tracking

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