CodeEntropy.entropy.water module

Water entropy aggregation.

This module wraps the waterEntropy routines and maps their outputs into the project ResultsReporter format.

class CodeEntropy.entropy.water.WaterEntropy(args: ~typing.Any, reporter: ~typing.Any, solver: ~collections.abc.Callable[[...], tuple[dict, ~typing.Any, ~typing.Any, ~typing.Any, ~typing.Any]] = <function get_interfacial_water_orient_entropy>)[source]

Bases: object

Compute and log water entropy contributions.

This class calls the external waterEntropy routine to compute:

  • orientational entropy per residue

  • translational vibrational entropy

  • rotational vibrational entropy

Then it logs residue-level entries and adds a group label.

calculate_and_log(universe: Any, start: int, end: int, step: int, group_id: int | None = None) → None[source]

Compute water entropy and write results to the data logger.

Parameters:

  • universe – MDAnalysis Universe containing water.

  • start – Start frame index.

  • end – End frame index.

  • step – Frame stride.

  • group_id – Group ID to assign all water contributions to.

class CodeEntropy.entropy.water.WaterEntropyInput(universe: Any, start: int, end: int, step: int, temperature: float, group_id: int | None = None)[source]

Bases: object

Inputs for water entropy computation.

Variables:

  • universe (Any) – MDAnalysis Universe containing the system.

  • start (int) – Start frame index (inclusive).

  • end (int) – End frame index (exclusive, or -1 depending on caller convention).

  • step (int) – Frame stride.

  • temperature (float) – Temperature in Kelvin.

  • group_id (int | None) – Group ID used for logging.

end: int
group_id: int | None = None
start: int
step: int
temperature: float
universe: Any