deepfold.losses.violation.within_residue_violations

deepfold.losses.violation.within_residue_violations(atom14_pred_positions: Tensor, atom14_atom_exists: Tensor, atom14_dists_lower_bound: Tensor, atom14_dists_upper_bound: Tensor, tighten_bounds_for_loss: float = 0.0, eps: float = 1e-10) → Dict[str, Tensor][source]

Loss to penalize steric clashes within residues.

This is a loss penalizing any steric violations or clashes of non-bonded atoms in a given peptide. This loss corresponds to the part with the same residues of equation 46 (Supplementary ‘1.9.11 Structural violations’).

Parameters:

  • atom14_pred_positions ([*, N, 14, 3]) – Predicted positions of atoms in global prediction frame.

  • atom14_atom_exists ([*, N, 14]) – Mask denoting whether atom at positions exists for given amino acid type

  • atom14_dists_lower_bound ([*, N, 14]) – Lower bound on allowed distances.

  • atom14_dists_upper_bound ([*, N, 14]) – Upper bound on allowed distances

  • tighten_bounds_for_loss ([*, N]) – Extra factor to tighten loss

Returns:

  • ‘per_atom_loss_sum’ ([*, N, 14]):

    sum of all clash losses per atom, shape

  • ’per_atom_clash_mask’ ([*, N, 14]):

    mask whether atom clashes with any other atom shape

Return type:

Dict containing