CodeEntropy.entropy.workflow module

Entropy manager orchestration.

This module defines EntropyWorkflow, which coordinates the end-to-end entropy workflow: - Determine trajectory bounds and frame count. - Build a reduced universe based on atom selection. - Identify molecule groups and hierarchy levels. - Optionally compute water entropy and adjust selection. - Execute the level DAG (matrix/state preparation). - Execute the entropy graph (entropy calculations and aggregation). - Finalize and persist results.

The manager intentionally delegates calculations to dedicated components.

class CodeEntropy.entropy.workflow.EntropyWorkflow(run_manager: Any, args: Any, universe: Any, reporter: Any, group_molecules: Any, dihedral_analysis: Any, universe_operations: Any)[source]

Bases: object

Coordinate entropy calculations across structural levels.

This class is responsible for orchestration and IO-level concerns (selection, grouping, running graphs, and finalizing results). Domain calculations live in dedicated components (LevelDAG, EntropyGraph, WaterEntropy, etc.).

execute() → None[source]

Run the full entropy workflow and emit results.

This orchestrates the complete entropy pipeline:

  1. Build trajectory slice.

  2. Apply atom and frame selection to create a reduced universe.

  3. Detect hierarchy levels.

  4. Group molecules.

  5. Split groups into water and non-water.

  6. Optionally compute water entropy (only if solute exists).

  7. Run level DAG and entropy graph.

  8. Finalize and persist results.

class CodeEntropy.entropy.workflow.TrajectorySlice(start: int, end: int, step: int, n_frames: int)[source]

Bases: object

Trajectory slicing parameters.

Variables:

  • start (int) – Inclusive start frame index.

  • end (int) – Exclusive end frame index (or a concrete index derived from args).

  • step (int) – Step size between frames.

  • n_frames (int) – Number of frames in the slice.

end: int
n_frames: int
start: int
step: int