torchref.refinement.targets.geometry.bonds module

class torchref.refinement.targets.geometry.bonds.BondTarget(model=None, verbose=0)

Bases: GeometryTarget

Bond length restraint target (Gaussian NLL).

NLL = 0.5 * ((d - d₀) / σ)² + log(σ) + 0.5 * log(2π)

name: str = 'geometry/bond'

__init__(model=None, 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.

forward()

Compute and return the loss. Override in subclasses.

stats()

Get bond restraint statistics.