CodeEntropy.entropy.nodes.vibrational module

Node for computing vibrational entropy from covariance matrices.

class CodeEntropy.entropy.nodes.vibrational.EntropyPair(trans: float, rot: float)

Bases: object

Container for paired translational and rotational entropy values.

Variables:

• trans (float) – Translational vibrational entropy value.

• rot (float) – Rotational vibrational entropy value.

rot: float

trans: float

class CodeEntropy.entropy.nodes.vibrational.VibrationalEntropyNode

Bases: object

Compute vibrational entropy from force/torque (and optional FT) covariances.

This node reads covariance matrices from a shared data mapping, computes translational and rotational vibrational entropy at requested hierarchy levels, and stores results back into the shared data structure.

The node supports:

• Force and torque covariance matrices (“force” / “torque”) at residue/polymer levels.

• United-atom per-residue covariances keyed by (group_id, residue_id).

• Optional combined force-torque covariance matrices (“forcetorque”) for the highest level when enabled via args.combined_forcetorque.

run(shared_data: MutableMapping[str, Any], **_: Any) → dict[str, Any]

Run vibrational entropy calculations and update the shared data mapping.

Parameters:

• shared_data – Mutable mapping containing inputs (covariances, groups, levels, args, etc.) and where outputs will be written.

• **_ – Unused keyword arguments, accepted for framework compatibility.

Returns:

A dict containing the computed vibrational entropy results under the key “vibrational_entropy”.

Raises:

ValueError – If an unknown level is encountered in the level list for a representative molecule.