Converts a `Protein` instance to a PDB string. Args: prot: The protein to convert to PDB. Returns: PDB string.

Conversion method of torsion angles to frames provided the backbone. Args: r: Backbone rigid groups. alpha: Torsion angles.

trace back dynamic programming path to diciper pairwise alignment */

trace back Smith-Waterman dynamic programming path to diciper * pairwise local alignment */

Contains the training pipeline. Can additionally evaluate model on a testset, using best weights achieved during training. Args: conf

Loss to penalize steric clashes within residues. This is a loss penalizing any steric violations or clashes of non-bonded atoms in a given pe

This is the same as the previous NWDP_TM, except for the lack of rotation * Input: vectors x, y, scale factor d02, and gap_open * Output: j2i[1:le

coords -> `pos_heavyatom` [B, num_res, num_atom, 3] tokens. -> `aa` [B, num_res] coord_mask -> `mask_heavyatom` [B, num_res,

Args: save_step_frequency: how often to save in steps prefix: add a prefix to the name, only used if

Initialize sampler. Args: cfg: inference config.

Args: c_hidden: Hidden channel dimension

Args: c_s: Single representation channel dimension c_z: Pair representation channel d

Args: c_s: Single representation channel dimension

Args: c_s: Single representation channel dimension c_z: Pair representation channel d