MHCXGraph.core.config.GraphConfig¶

class MHCXGraph.core.config.GraphConfig(chains: Iterable[str] | None = None, include_waters: bool = True, include_noncanonical_residues: bool = True, include_ligands: bool = True, residue_distance_cutoff: float = 10.0, store_distance_matrix: bool = True, compute_rsa: bool = True, model_index: int = 0, allow_empty_chains: bool = False, granularity: Literal['all_atoms', 'backbone', 'side_chain', 'ca_only'] = 'all_atoms', verbose: bool = False, make_virtual_cb_for_gly: bool = True, max_gap_helix: int = 0)[source]¶

Unified configuration for building residue-level graphs from PDB/mmCIF files.

Parameters:

chains (collections.abc.Iterable[str] | None) – Iterable of chain IDs to include. None includes all chains in the selected model.
include_waters (bool) – If True, includes water molecules (HOH) as nodes and residue–water edges.
residue_distance_cutoff (float) – Residue–residue and Water-residue centroid distance cutoff (Å) for adding edges.
store_distance_matrix (bool) – If True, keeps the residue–residue distance matrix in the returned object.
compute_rsa (bool) – If True, computes ASA and RSA per residue.
model_index (int) – Model index to load from the structure file.
allow_empty_chains (bool) – If False, raises when requested chains are not found.
granularity (Literal['all_atoms', 'backbone', 'side_chain', 'ca_only']) – Centroid policy for node coordinates. See Granularity for options.
verbose (bool) – Enables additional logging when supported by the caller.

__init__(chains: Iterable[str] | None = None, include_waters: bool = True, include_noncanonical_residues: bool = True, include_ligands: bool = True, residue_distance_cutoff: float = 10.0, store_distance_matrix: bool = True, compute_rsa: bool = True, model_index: int = 0, allow_empty_chains: bool = False, granularity: Literal['all_atoms', 'backbone', 'side_chain', 'ca_only'] = 'all_atoms', verbose: bool = False, make_virtual_cb_for_gly: bool = True, max_gap_helix: int = 0) → None¶

Methods

__init__([chains, include_waters, ...])

Attributes

`allow_empty_chains`
`chains`
`compute_rsa`
`granularity`
`include_ligands`
`include_noncanonical_residues`
`include_waters`
`make_virtual_cb_for_gly`
`max_gap_helix`
`model_index`
`residue_distance_cutoff`
`store_distance_matrix`
`verbose`