deepfold.relax.amber_minimize.run_pipeline

deepfold.relax.amber_minimize.run_pipeline(prot: Protein, stiffness: float, use_gpu: bool, max_outer_iterations: int = 1, place_hydrogens_every_iteration: bool = True, max_iterations: int = 0, tolerance: float = 2.39, restraint_set: str = 'non_hydrogen', max_attempts: int = 100, checks: bool = True, exclude_residues: Sequence[int] | None = None)

Run iterative amber relax.

Successive relax iterations are performed until all violations have been resolved. Each iteration involves a restrained Amber minimization, with restraint exclusions determined by violation-participating residues.

Parameters:

• prot – A protein to be relaxed.

• stiffness – kcal/mol A**2, the restraint stiffness.

• use_gpu – Whether to run on GPU

• max_outer_iterations – The maximum number of iterative minimization.

• place_hydrogens_every_iteration – Whether hydrogens are re-initialized prior to every minimization.

• max_iterations – An int specifying the maximum number of L-BFGS steps per relax iteration. A value of 0 specifies no limit.

• tolerance – kcal/mol, the energy tolerance of L-BFGS. The default value is the OpenMM default.

• restraint_set – The set of atoms to restrain.

• max_attempts – The maximum number of minimization attempts per iteration.

• checks – Whether to perform cleaning checks.

• exclude_residues – An optional list of zero-indexed residues to exclude from restraints.

Returns:

A dictionary of output values.

Return type:

out