deepfold.relax.relax.AmberRelaxation

class deepfold.relax.relax.AmberRelaxation(*, max_iterations: int, tolerance: float, stiffness: float, exclude_residues: Sequence[int], max_outer_iterations: int, use_gpu: bool)[source]

Amber relaxation.

__init__(*, max_iterations: int, tolerance: float, stiffness: float, exclude_residues: Sequence[int], max_outer_iterations: int, use_gpu: bool)[source]

Initialize Amber Relaxer.

Parameters:

  • max_iterations – Maximum number of L-BFGS iterations. 0 means no max.

  • tolerance – kcal/mol, the energy tolerance of L-BFGS.

  • stiffness – kcal/mol A**2, spring constant of heavy atom restraining potential.

  • exclude_residues – Residues to exclude from per-atom restraining. Zero-indexed.

  • max_outer_iterations – Maximum number of violation-informed relax iterations. A value of 1 will run the non-iterative procedure used in CASP14. Use 20 so that >95% of the bad cases are relaxed. Relax finishes as soon as there are no violations, hence in most cases this causes no slowdown. In the worst case we do 20 outer iterations.

  • use_gpu – Whether to run on GPU

Methods

__init__(*, max_iterations, tolerance, ...)

Initialize Amber Relaxer.

process(*, prot)

Runs Amber relax on a prediction, adds hydrogens, returns PDB string.