torchref.refinement.targets.geometry.torsions module

class torchref.refinement.targets.geometry.torsions.TorsionTarget(model=None, verbose=0, w_cis_proline=0.05, w_cis_general=0.0005)

Bases: GeometryTarget

Torsion angle restraint target.

Handles all torsion restraints in one target:

• Intra-residue & disulfide torsions: unimodal von Mises NLL with periodicity handling.

• Omega (peptide bond) torsions: cis/trans von Mises mixture, so both cis and trans conformations are stable wells and the X-ray data decides which one to adopt.

Parameters:

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

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

• w_cis_proline (float, optional) – Prior weight for cis conformation at pre-proline peptide bonds. Default 0.05 (~5% of X-Pro bonds are cis in the PDB).

• w_cis_general (float, optional) – Prior weight for cis conformation at non-proline peptide bonds. Default 0.0005 (~0.05% of non-Pro bonds are cis in the PDB).

name: str = 'geometry/torsion'

__init__(model=None, verbose=0, w_cis_proline=0.05, w_cis_general=0.0005)

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 torsion angle statistics.