CodeEntropy.levels.nodes.axes_topology module¶

Build static axes-topology metadata for frame covariance calculations.

This module caches topology-only atom-index relationships needed by customised axes calculations. The cache avoids repeated MDAnalysis selection parsing inside the frame-local covariance loop while preserving frame-dependent positions, forces, centres, axes, torques, and moments of inertia.

class CodeEntropy.levels.nodes.axes_topology.AxesTopology(ua: dict[tuple[int, int, int], ~CodeEntropy.levels.nodes.axes_topology.UAAxesTopology] = <factory>, residue: dict[tuple[int, int], ~CodeEntropy.levels.nodes.axes_topology.ResidueAxesTopology] = <factory>)[source]¶

Bases: object

Cached axes topology for frame covariance calculations.

Variables:

ua (dict[tuple[int, int, int], CodeEntropy.levels.nodes.axes_topology.UAAxesTopology]) – Mapping from (mol_id, local_residue_id, ua_id) to cached united-atom axes topology.
residue (dict[tuple[int, int], CodeEntropy.levels.nodes.axes_topology.ResidueAxesTopology]) – Mapping from (mol_id, local_residue_id) to cached residue axes topology.

residue: dict[tuple[int, int], ResidueAxesTopology]¶

ua: dict[tuple[int, int, int], UAAxesTopology]¶

class CodeEntropy.levels.nodes.axes_topology.BuildAxesTopologyNode[source]¶

Bases: object

Build static customised-axes topology before frame covariance execution.

run(shared_data: dict[str, Any]) → dict[str, Any][source]¶

Build cached axes topology and write it into shared data.

The cache is only populated when args.customised_axes is true. When customised axes are disabled, an empty cache is still written so later stages can read shared_data["axes_topology"] safely.

Parameters:: shared_data – Shared workflow data containing args and, when customised axes are enabled, reduced_universe, levels, and beads.
Returns:: Dict containing the cached axes_topology object.

class CodeEntropy.levels.nodes.axes_topology.ResidueAxesTopology(residue_heavy_indices: ndarray, residue_ua_masses: ndarray, has_neighbor_bonds: bool)[source]¶

Bases: object

Static topology required to compute customised residue axes.

Variables:

residue_heavy_indices (numpy.ndarray) – Heavy atom indices in the residue.
residue_ua_masses (numpy.ndarray) – UA masses for heavy atoms in the residue.
has_neighbor_bonds (bool) – Whether the residue is bonded to a neighbouring residue according to the original customised residue-axis selection.

has_neighbor_bonds: bool¶

residue_heavy_indices: ndarray¶

residue_ua_masses: ndarray¶

class CodeEntropy.levels.nodes.axes_topology.UAAxesTopology(heavy_atom_index: int, ua_atom_indices: ndarray, ua_all_atom_indices: ndarray, bonded_heavy_indices: ndarray, bonded_light_indices: ndarray, residue_heavy_indices: ndarray, residue_ua_masses: ndarray)[source]¶

Bases: object

Static topology required to compute customised united-atom axes.

Variables:

heavy_atom_index (int) – Reduced-universe atom index for the UA heavy atom.
ua_atom_indices (numpy.ndarray) – Atom indices for the UA heavy atom and its bonded hydrogens/light atoms.
ua_all_atom_indices (numpy.ndarray) – Atom indices for the UA heavy atom, bonded heavy atoms, and bonded hydrogens/light atoms.
bonded_heavy_indices (numpy.ndarray) – Heavy atoms bonded to the UA heavy atom.
bonded_light_indices (numpy.ndarray) – Hydrogens/light atoms bonded to the UA heavy atom.
residue_heavy_indices (numpy.ndarray) – Heavy atoms in the parent residue.
residue_ua_masses (numpy.ndarray) – UA masses for heavy atoms in the parent residue.

bonded_heavy_indices: ndarray¶

bonded_light_indices: ndarray¶

heavy_atom_index: int¶

residue_heavy_indices: ndarray¶

residue_ua_masses: ndarray¶

ua_all_atom_indices: ndarray¶

ua_atom_indices: ndarray¶