torchref.refinement.targets.adp.similarity module

class torchref.refinement.targets.adp.similarity.ADPSimilarityTarget(model=None, simu_sigma=2.0, verbose=0)

Bases: ADPTarget

ADP Similarity restraint (SIMU in Phenix/SHELX).

Restrains B-factors of bonded atoms to be similar. NLL = 0.5 * ((B_i - B_j) / σ)² + log(σ) + 0.5 * log(2π)

Tunable parameters (as buffers): - _simu_sigma: float, sigma for B-factor differences (default 2.0 Ų)

name: str = 'adp/simu'

__init__(model=None, simu_sigma=2.0, verbose=0)

Initialize model target.

Parameters:

• model (Model, optional) – Reference to the Model object (optional for empty init).

• verbose (int, optional) – Verbosity level. Default is 0.

property simu_sigma: float

Get SIMU sigma value.

forward()

Compute and return the loss. Override in subclasses.

stats()

Get SIMU restraint statistics.