deepfold.relax.amber_minimize

Restrained Amber Minimization of a structure.

Functions

clean_protein(prot[, checks])	Adds missing atoms to Protein instance.
find_violations(prot_np)	Analyzes a protein and returns structural violation information.
get_violation_metrics(prot)	Computes violation and alignment metrics.
make_atom14_positions(prot)	Constructs denser atom positions (14 dimensions instead of 37).
run_pipeline(prot, stiffness, use_gpu[, ...])	Run iterative amber relax.
will_restrain(atom, rset)	Returns True if the atom will be restrained by the given restraint set.