CodeEntropy.levels.nodes.conformations module

Compute conformational states for configurational entropy calculations.

This module defines a static DAG node that scans the trajectory and builds conformational state descriptors (united-atom and residue level). The resulting states are stored in shared_data for later use by configurational entropy calculations.

class CodeEntropy.levels.nodes.conformations.ComputeConformationalStatesNode(universe_operations: Any)

Bases: object

Static node that computes conformational states from trajectory dihedrals.

Produces:

shared_data[“conformational_states”] = {“ua”: states_ua, “res”: states_res} shared_data[“flexible_dihedrals”] = {“ua: flexible_ua, “res”: flexible_res}

Where:

• states_ua is a dict keyed by (group_id, local_residue_id)

• states_res is a list-like structure indexed by group_id (or equivalent)

• flexible_ua is a dict keyed by (group_id, local_residue_id)

• flexible_res is a list-like structure indexed by group_id (or equivalent)

run(shared_data: dict[str, Any], *, progress: object | None = None) → dict[str, dict[str, Any]]

Compute conformational states and store them in shared_data.

Parameters:

• shared_data – Shared data dictionary. Requires: - “reduced_universe” - “levels” - “groups” - “n_frames” - “args” with attribute “bin_width”

• progress – Optional progress sink provided by ResultsReporter.progress().

Returns:

Dict containing “conformational_states” (also written into shared_data).

class CodeEntropy.levels.nodes.conformations.ConformationalStateConfig(n_frames: int, bin_width: int)

Bases: object

Configuration for conformational state construction.

Variables:

• n_frames (int) – Number of frames to be analyised.

• bin_width (int) – Histogram bin width in degrees.

bin_width: int

n_frames: int