openfold.np.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.
clean_protein(prot, checks=True)

Adds missing atoms to Protein instance.

Parameters:

  • prot (Protein) – A protein.Protein instance.

  • checks (bool) – A bool specifying whether to add additional checks to the cleaning process.

Returns:

A string of the cleaned protein.

Return type:

pdb_string

find_violations(prot_np)

Analyzes a protein and returns structural violation information.

Parameters:

prot_np (Protein) – A protein.

Returns:

A dict of structure components with structural violations. violation_metrics: A dict of violation metrics.

Return type:

violations

get_violation_metrics(prot)

Computes violation and alignment metrics.

Parameters:

prot (Protein)

make_atom14_positions(prot)

Constructs denser atom positions (14 dimensions instead of 37).

run_pipeline(prot, stiffness, use_gpu, max_outer_iterations=1, place_hydrogens_every_iteration=True, max_iterations=0, tolerance=2.39, restraint_set='non_hydrogen', max_attempts=100, checks=True, exclude_residues=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 (Protein) – A protein to be relaxed.

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

  • use_gpu (bool) – Whether to run on GPU

  • max_outer_iterations (int) – The maximum number of iterative minimization.

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

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

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

  • restraint_set (str) – The set of atoms to restrain.

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

  • checks (bool) – Whether to perform cleaning checks.

  • exclude_residues (Sequence[int] | None) – An optional list of zero-indexed residues to exclude from restraints.

Returns:

A dictionary of output values.

Return type:

out

will_restrain(atom, rset)

Returns True if the atom will be restrained by the given restraint set.

Parameters:

  • atom (Atom)

  • rset (str)

Return type:

bool