MHCXGraph.core.config.make_default_config

MHCXGraph.core.config.make_default_config(*, edge_threshold: float = 10.0, granularity: Literal['all_atoms', 'backbone', 'side_chain', 'ca_only'] = 'all_atoms', chains: Iterable[str] | None = None, compute_rsa: bool = True, make_virtual_cb_for_gly: bool = True, include_noncanonical_residues: bool = True, include_ligands: bool = True, include_waters: bool = True, verbose: bool = False, max_gap_helix: int = 0) → GraphConfig[source]

Helper for creating a GraphConfig with common defaults.

Parameters:

  • edge_threshold – Residue–residue distance cutoff (Å).

  • granularity – Centroid policy for node coordinates.

  • include_waters – If True, includes water molecules as nodes.

  • chains – Iterable of chain IDs to include; None includes all chains.

  • compute_rsa – If True, computes ASA/RSA per residue.

Returns:

Ready-to-use configuration instance.

Return type:

GraphConfig