MHCXGraph.scripts.renumber_MHCII_imgt¶

MHCXGraph.scripts.renumber_MHCII_imgt.align_query_to_template(query_seq: str, template_ungapped: str)[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.choose_best_template_for_chain(query_seq: str, templates_for_type: list[dict]) → dict[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.compute_alignment_stats(aln) → dict[str, float][source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.continue_numbering_from_unmatched(aa_residues_in_order, numbering_map, projected_residues, unmatched_query_positions, debug=False)[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.detect_mhcII_chains(model, templates, debug: bool = False)[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.get_chain_polymer_residues(chain) → list[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.get_chain_sequence_and_residues(chain) → tuple[str, list][source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.load_mhcii_templates(display_csv: Path, numbering_csv: Path)[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.load_structure(path: str, structure_id: str = 'structure')[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.main()[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.parse_imgt_label(label: str) → tuple[int, str][source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.print_alignment_blocks(label: str, seq: str, width: int = 80)[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.print_debug_alignment(chain_id: str, mhc_type: str, template_name: str, aln, gapped_template: str, projected_query_chars: list[str], numbering: list[str])[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.process_structure_file_mhcii(input_path: str, output_path: str, templates, alpha_chain: str = None, beta_chain: str = None, debug: bool = False, warn_score: float = 50.0)[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.project_query_onto_gapped_template(gapped_template: str, numbering: list[str], aligned_template_ungapped: str, aligned_query: str, chain_residues: list)[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.renumber_chain_from_projection(chain, projected_residues, numbering_map, debug=False)[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.residue_to_one_letter(residue) → str[source]¶

MHCXGraph.scripts.renumber_MHCII_imgt.save_structure(structure, output_path: str)[source]¶

Functions¶

`align_query_to_template`(query_seq, ...)
`choose_best_template_for_chain`(query_seq, ...)
`compute_alignment_stats`(aln)
`continue_numbering_from_unmatched`(...[, debug])
`detect_mhcII_chains`(model, templates[, debug])
`get_chain_polymer_residues`(chain)
`get_chain_sequence_and_residues`(chain)
`load_mhcii_templates`(display_csv, numbering_csv)
`load_structure`(path[, structure_id])
`main`()
`parse_imgt_label`(label)
`print_alignment_blocks`(label, seq[, width])
`print_debug_alignment`(chain_id, mhc_type, ...)
`process_structure_file_mhcii`(input_path, ...)
`project_query_onto_gapped_template`(...)
`renumber_chain_from_projection`(chain, ...[, ...])
`residue_to_one_letter`(residue)
`save_structure`(structure, output_path)