Index

_

__init__() (MHCXGraph.classes.graph.AssociatedGraph method) (MHCXGraph.classes.graph.Graph method) (MHCXGraph.classes.graph.GraphData method) (MHCXGraph.core.config.DSSPConfig method) (MHCXGraph.core.config.GraphConfig method) (MHCXGraph.core.pdb_graph_builder.AtomBundle method) (MHCXGraph.core.pdb_graph_builder.BuiltGraph method) (MHCXGraph.core.pdb_graph_builder.FixedPDBIO method) (MHCXGraph.core.pdb_graph_builder.NodeCoords method) (MHCXGraph.core.pdb_graph_builder.PDBGraphBuilder method) (MHCXGraph.core.pdb_graph_builder.ResidueInfo method) (MHCXGraph.core.pdb_graph_builder.StructureDict method) (MHCXGraph.core.residue_tracking.ResidueTracker method) (MHCXGraph.core.residue_tracking.TrackCtx method) (MHCXGraph.core.tracking.Tracker method) (MHCXGraph.core.tracking.TrackerConfig method) (MHCXGraph.utils.logging_utils.ConsoleFilter method) (MHCXGraph.utils.logging_utils.VerboseLoggerAdapter method)

A

align_all_frames() (MHCXGraph.classes.graph.AssociatedGraph method) align_query_to_template() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] allow_empty_chains (MHCXGraph.core.config.GraphConfig attribute)

associated_graphs (MHCXGraph.classes.graph.AssociatedGraph attribute), [1] AssociatedGraph (class in MHCXGraph.classes.graph), [1] association_config (MHCXGraph.classes.graph.AssociatedGraph attribute), [1] association_product() (in module MHCXGraph.utils.tools), [1] AtomBundle (class in MHCXGraph.core.pdb_graph_builder), [1]

B

build_association_config() (in module MHCXGraph.workflow.manifest), [1] build_component_matrix() (in module MHCXGraph.scripts.create_heatmaps), [1] build_graph() (MHCXGraph.core.pdb_graph_builder.PDBGraphBuilder method)

build_graph_from_cross_combos() (in module MHCXGraph.utils.tools), [1] build_graph_with_config() (in module MHCXGraph.core.pipeline), [1] build_threshold_vector() (in module MHCXGraph.utils.tools), [1] BuiltGraph (class in MHCXGraph.core.pdb_graph_builder), [1]

C

ca_cb_map (MHCXGraph.core.pdb_graph_builder.AtomBundle attribute) ca_coord (MHCXGraph.core.pdb_graph_builder.NodeCoords attribute) canonical_aminoacid_residues (MHCXGraph.core.pdb_graph_builder.ResidueInfo attribute) capture_c_stderr() (in module MHCXGraph.core.pdb_graph_builder), [1] cb_coord (MHCXGraph.core.pdb_graph_builder.NodeCoords attribute) cb_is_virtual (MHCXGraph.core.pdb_graph_builder.NodeCoords attribute) chain_signature() (in module MHCXGraph.utils.analysis), [1] chains (MHCXGraph.core.config.GraphConfig attribute) (MHCXGraph.core.pdb_graph_builder.StructureDict attribute) chains_obj (MHCXGraph.core.pdb_graph_builder.StructureDict attribute) check_res_inconsistencies() (in module MHCXGraph.core.pdb_graph_builder), [1] choose_best_template_for_chain() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] chunk_id (MHCXGraph.core.residue_tracking.TrackCtx attribute) clean_graph_name() (in module MHCXGraph.app), [1] collect_selected_files_from_manifest() (in module MHCXGraph.utils.preprocessing), [1] combo_residues() (in module MHCXGraph.core.residue_tracking), [1] combos_built() (MHCXGraph.core.residue_tracking.ResidueTracker method) comp_id (MHCXGraph.core.residue_tracking.TrackCtx attribute) component_selected() (MHCXGraph.core.residue_tracking.ResidueTracker method)

component_skipped() (MHCXGraph.core.residue_tracking.ResidueTracker method) compute_alignment_stats() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] compute_distmat() (in module MHCXGraph.core.subgraphs), [1] compute_rsa (MHCXGraph.core.config.GraphConfig attribute) config (MHCXGraph.classes.graph.Graph attribute), [1] ConsoleFilter (class in MHCXGraph.utils.logging_utils), [1] contact_map (MHCXGraph.classes.graph.GraphData attribute) contact_map_from_graph() (in module MHCXGraph.core.contact_map), [1] continue_numbering_from_unmatched() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] convert_edges_to_residues() (in module MHCXGraph.utils.tools), [1] create_coherent_matrices() (in module MHCXGraph.utils.tools), [1] create_distance_matrix() (in module MHCXGraph.scripts.create_heatmaps), [1] create_graph() (in module MHCXGraph.utils.tools), [1] create_graphs() (in module MHCXGraph.utils.preprocessing), [1] create_heatmap() (in module MHCXGraph.scripts.create_heatmaps), [1] create_master_dashboard() (in module MHCXGraph.app), [1] create_pdb_per_protein() (MHCXGraph.classes.graph.AssociatedGraph method) create_subgraph() (MHCXGraph.classes.graph.Graph method) cross_protein_triads() (in module MHCXGraph.utils.tools), [1]

D

detect_mhci_chain() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] detect_mhcII_chains() (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] distance_matrix (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2]

dssp_df (MHCXGraph.classes.graph.Graph attribute), [1] (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2] DSSPConfig (class in MHCXGraph.core.config), [1] dump_json() (MHCXGraph.core.residue_tracking.ResidueTracker method)

E

evaluate_all_frames_nodes() (in module MHCXGraph.utils.analysis), [1] evaluate_all_frames_nodes_weighted() (in module MHCXGraph.utils.analysis), [1] evaluate_frame_nodes() (in module MHCXGraph.utils.analysis), [1] executable (MHCXGraph.core.config.DSSPConfig attribute) execute_step() (in module MHCXGraph.utils.tools), [1] extract_interface_subgraph() (in module MHCXGraph.core.subgraphs), [1] extract_k_hop_subgraph() (in module MHCXGraph.core.subgraphs), [1] extract_original_graph_info() (in module MHCXGraph.scripts.create_heatmaps), [1] extract_subgraph() (in module MHCXGraph.core.subgraphs), [1] extract_subgraph_by_bond_type() (in module MHCXGraph.core.subgraphs), [1]

extract_subgraph_by_sequence_position() (in module MHCXGraph.core.subgraphs), [1] extract_subgraph_from_atom_types() (in module MHCXGraph.core.subgraphs), [1] extract_subgraph_from_chains() (in module MHCXGraph.core.subgraphs), [1] extract_subgraph_from_node_list() (in module MHCXGraph.core.subgraphs), [1] extract_subgraph_from_point() (in module MHCXGraph.core.subgraphs), [1] extract_subgraph_from_residue_types() (in module MHCXGraph.core.subgraphs), [1] extract_subgraph_from_secondary_structure() (in module MHCXGraph.core.subgraphs), [1] extract_surface_subgraph_asa() (in module MHCXGraph.core.subgraphs), [1] extract_surface_subgraph_rsa() (in module MHCXGraph.core.subgraphs), [1] extract_unique_aminoacids() (in module MHCXGraph.scripts.create_heatmaps), [1]

F

filter() (MHCXGraph.utils.logging_utils.ConsoleFilter method) filter_maps_by_nodes() (in module MHCXGraph.utils.tools), [1] find_class() (in module MHCXGraph.utils.tools), [1]

find_triads() (in module MHCXGraph.utils.tools), [1] FixedPDBIO (class in MHCXGraph.core.pdb_graph_builder), [1] frame_accepted() (MHCXGraph.core.residue_tracking.ResidueTracker method) frame_id (MHCXGraph.core.residue_tracking.TrackCtx attribute)

G

generate_frames() (in module MHCXGraph.utils.tools), [1] get_chain_polymer_residues() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] get_chain_sequence_and_residues() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] get_current() (in module MHCXGraph.core.tracking), [1] get_dashboard_data() (MHCXGraph.classes.graph.AssociatedGraph method) get_exposed_residues() (in module MHCXGraph.utils.preprocessing), [1] get_log() (in module MHCXGraph.utils.logging_utils), [1] get_memory_usage_mb() (in module MHCXGraph.utils.tools), [1] get_protein_keys() (in module MHCXGraph.utils.analysis), [1] get_subgraph() (MHCXGraph.classes.graph.Graph method)

get_user_selection() (in module MHCXGraph.io_utils.pdb_io), [1] Granularity (in module MHCXGraph.core.config) granularity (MHCXGraph.core.config.GraphConfig attribute) Graph (class in MHCXGraph.classes.graph), [1] graph (MHCXGraph.classes.graph.Graph attribute), [1] (MHCXGraph.classes.graph.GraphData attribute) (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2] graph_path (MHCXGraph.classes.graph.Graph attribute), [1] GraphConfig (class in MHCXGraph.core.config), [1] GraphData (class in MHCXGraph.classes.graph), [1] graphs (MHCXGraph.classes.graph.AssociatedGraph attribute), [1] graphs_data (MHCXGraph.classes.graph.AssociatedGraph attribute), [1]

I

id (MHCXGraph.classes.graph.GraphData attribute) include_ligands (MHCXGraph.core.config.GraphConfig attribute) include_noncanonical_residues (MHCXGraph.core.config.GraphConfig attribute) include_waters (MHCXGraph.core.config.GraphConfig attribute)

init_tracker() (in module MHCXGraph.core.tracking), [1] inject_fullscreen_css() (in module MHCXGraph.utils.pyvis_inject), [1] inject_std_hover() (in module MHCXGraph.utils.pyvis_inject), [1] ivw_mean_proportions() (in module MHCXGraph.utils.analysis), [1]

L

ligands (MHCXGraph.core.pdb_graph_builder.ResidueInfo attribute) list_pdb_files() (in module MHCXGraph.io_utils.pdb_io), [1] list_struct_files() (in module MHCXGraph.utils.preprocessing), [1] load() (MHCXGraph.core.pdb_graph_builder.PDBGraphBuilder method) load_manifest() (in module MHCXGraph.workflow.manifest), [1] load_mhci_templates() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1]

load_mhcii_templates() (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] load_pyvis_std_js() (in module MHCXGraph.utils.pyvis_inject), [1] load_structure() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] log (in module MHCXGraph.core.pdb_graph_builder) (in module MHCXGraph.core.subgraphs) LogicError, [1]

M

main() (in module MHCXGraph.app), [1] (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] make_default_config() (in module MHCXGraph.core.config), [1] make_virtual_cb_for_gly (MHCXGraph.core.config.GraphConfig attribute) mark() (in module MHCXGraph.core.tracking), [1] (MHCXGraph.core.tracking.Tracker method) max_gap_helix (MHCXGraph.core.config.GraphConfig attribute) MHCXGraph module MHCXGraph.app module MHCXGraph.classes module MHCXGraph.classes.graph module MHCXGraph.cli module MHCXGraph.cli.cli_parser module MHCXGraph.core module MHCXGraph.core.config module MHCXGraph.core.contact_map module MHCXGraph.core.metadata module MHCXGraph.core.pdb_graph_builder module MHCXGraph.core.pipeline module MHCXGraph.core.residue_tracking module MHCXGraph.core.subgraphs module MHCXGraph.core.tracking module MHCXGraph.io_utils module MHCXGraph.io_utils.pdb_io module MHCXGraph.scripts module MHCXGraph.scripts.create_heatmaps module MHCXGraph.scripts.renumber_MHCI_imgt module MHCXGraph.scripts.renumber_MHCII_imgt module

MHCXGraph.utils module MHCXGraph.utils.analysis module MHCXGraph.utils.logging_utils module MHCXGraph.utils.preprocessing module MHCXGraph.utils.pyvis_inject module MHCXGraph.utils.tools module MHCXGraph.workflow module MHCXGraph.workflow.association module MHCXGraph.workflow.manifest module model_index (MHCXGraph.core.config.GraphConfig attribute) module MHCXGraph MHCXGraph.app MHCXGraph.classes MHCXGraph.classes.graph MHCXGraph.cli MHCXGraph.cli.cli_parser MHCXGraph.core MHCXGraph.core.config MHCXGraph.core.contact_map MHCXGraph.core.metadata MHCXGraph.core.pdb_graph_builder MHCXGraph.core.pipeline MHCXGraph.core.residue_tracking MHCXGraph.core.subgraphs MHCXGraph.core.tracking MHCXGraph.io_utils MHCXGraph.io_utils.pdb_io MHCXGraph.scripts MHCXGraph.scripts.create_heatmaps MHCXGraph.scripts.renumber_MHCI_imgt MHCXGraph.scripts.renumber_MHCII_imgt MHCXGraph.utils MHCXGraph.utils.analysis MHCXGraph.utils.logging_utils MHCXGraph.utils.preprocessing MHCXGraph.utils.pyvis_inject MHCXGraph.utils.tools MHCXGraph.workflow MHCXGraph.workflow.association MHCXGraph.workflow.manifest

N

name (MHCXGraph.classes.graph.GraphData attribute) node_centroids (MHCXGraph.core.pdb_graph_builder.AtomBundle attribute) (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2] node_similarity_for_protein() (in module MHCXGraph.utils.analysis), [1]

NodeCoords (class in MHCXGraph.core.pdb_graph_builder), [1] noncanonical_aminoacid_residues (MHCXGraph.core.pdb_graph_builder.ResidueInfo attribute) none_or_float() (in module MHCXGraph.cli.cli_parser), [1] normalize_numbering_column() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1]

O

output_path (MHCXGraph.classes.graph.AssociatedGraph attribute), [1]

P

parse_args() (in module MHCXGraph.cli.cli_parser), [1] parse_imgt_label() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] parse_node() (in module MHCXGraph.utils.tools), [1] parse_node_label() (in module MHCXGraph.core.residue_tracking), [1] pdb_df (MHCXGraph.classes.graph.Graph attribute), [1] pdb_file (MHCXGraph.classes.graph.GraphData attribute) PDBGraphBuilder (class in MHCXGraph.core.pdb_graph_builder), [1] print_alignment_blocks() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1]

print_debug_alignment() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] process_chunk() (in module MHCXGraph.utils.tools), [1] process_directories() (in module MHCXGraph.scripts.create_heatmaps), [1] process_structure_file_mhci() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] process_structure_file_mhcii() (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] project_nodes_instances() (in module MHCXGraph.utils.analysis), [1] project_query_onto_gapped_template() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] protein_i (MHCXGraph.core.residue_tracking.TrackCtx attribute) ProteinGraphConfigurationError, [1]

R

raw_df (MHCXGraph.core.pdb_graph_builder.AtomBundle attribute) raw_pdb_df (MHCXGraph.classes.graph.Graph attribute), [1] (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2] rebuild_cross_combos() (in module MHCXGraph.utils.tools), [1] renumber() (in module MHCXGraph.app), [1] renumber_chain_from_projection() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] residue_centroids (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2] residue_distance_cutoff (MHCXGraph.core.config.GraphConfig attribute) residue_index (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2] residue_key() (in module MHCXGraph.core.residue_tracking), [1] residue_map (MHCXGraph.classes.graph.GraphData attribute) residue_map_all (MHCXGraph.classes.graph.GraphData attribute) residue_to_one_letter() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1]

residue_to_tuple() (in module MHCXGraph.utils.tools), [1] ResidueInfo (class in MHCXGraph.core.pdb_graph_builder), [1] residues (MHCXGraph.core.pdb_graph_builder.StructureDict attribute) ResidueTracker (class in MHCXGraph.core.residue_tracking), [1] resolve_from_pdb_dfs() (MHCXGraph.core.residue_tracking.ResidueTracker method) resolve_selection_params_for_file() (in module MHCXGraph.utils.preprocessing), [1] rsa (MHCXGraph.classes.graph.GraphData attribute) run() (in module MHCXGraph.app), [1] run_association_task() (in module MHCXGraph.workflow.association), [1] run_id (MHCXGraph.core.residue_tracking.TrackCtx attribute) run_multiple_mode() (in module MHCXGraph.app), [1] run_name (MHCXGraph.classes.graph.AssociatedGraph attribute), [1] run_pairwise_mode() (in module MHCXGraph.app), [1] run_screening_mode() (in module MHCXGraph.app), [1]

S

save() (in module MHCXGraph.core.tracking), [1] (MHCXGraph.core.tracking.Tracker method) save_filtered_pdb() (MHCXGraph.classes.graph.Graph method) save_structure() (in module MHCXGraph.scripts.renumber_MHCI_imgt), [1] (in module MHCXGraph.scripts.renumber_MHCII_imgt), [1] secondary_structure() (in module MHCXGraph.core.metadata), [1] set_enabled() (in module MHCXGraph.core.tracking), [1] setup_logging() (in module MHCXGraph.utils.logging_utils), [1] setup_trackers() (in module MHCXGraph.app), [1] sorted_nodes (MHCXGraph.classes.graph.GraphData attribute)

stage (MHCXGraph.core.residue_tracking.TrackCtx attribute) step_id (MHCXGraph.core.residue_tracking.TrackCtx attribute) store_distance_matrix (MHCXGraph.core.config.GraphConfig attribute) str2bool() (in module MHCXGraph.cli.cli_parser), [1] structure (MHCXGraph.core.pdb_graph_builder.PDBGraphBuilder attribute) StructureDict (class in MHCXGraph.core.pdb_graph_builder), [1] subgraphs (MHCXGraph.classes.graph.Graph attribute), [1] summarize_frame_nodes() (in module MHCXGraph.utils.analysis), [1] sym_from_packed_bool() (in module MHCXGraph.utils.tools), [1] sym_from_packed_float() (in module MHCXGraph.utils.tools), [1]

T

to_graphml() (MHCXGraph.core.pdb_graph_builder.PDBGraphBuilder static method) to_json() (MHCXGraph.core.pdb_graph_builder.PDBGraphBuilder static method) track() (in module MHCXGraph.core.tracking), [1] (MHCXGraph.core.tracking.Tracker method) TrackCtx (class in MHCXGraph.core.residue_tracking), [1] tracked() (in module MHCXGraph.core.tracking), [1]

Tracker (class in MHCXGraph.core.tracking), [1] TrackerConfig (class in MHCXGraph.core.tracking) triad_chirality_with_cb() (in module MHCXGraph.utils.tools), [1] triad_filtered() (MHCXGraph.core.residue_tracking.ResidueTracker method) triad_residues_from_absolute() (in module MHCXGraph.core.residue_tracking), [1] triads_built() (MHCXGraph.core.residue_tracking.ResidueTracker method)

U

unique_chain_signatures() (in module MHCXGraph.utils.analysis), [1]

V

value_to_class() (in module MHCXGraph.utils.tools), [1] verbose (MHCXGraph.core.config.GraphConfig attribute)

VerboseLoggerAdapter (class in MHCXGraph.utils.logging_utils), [1] vinfo() (MHCXGraph.utils.logging_utils.VerboseLoggerAdapter method)

W

water_centroids (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2] water_index (MHCXGraph.core.pdb_graph_builder.BuiltGraph attribute), [1], [2] waters (MHCXGraph.core.pdb_graph_builder.ResidueInfo attribute)

wmean() (in module MHCXGraph.utils.analysis), [1] wmedian() (in module MHCXGraph.utils.analysis), [1] wstd() (in module MHCXGraph.utils.analysis), [1] wtrimmed_mean() (in module MHCXGraph.utils.analysis), [1]