Parses the data file from PDB that lists which PDB ids are obsolete.

Parses release dates file, returns a mapping from PDBs to release dates.

Auxiliary function for performing additional processing steps on the sampled angles. One example would be to ensure sampled angles ar

Tries to extract template features from a single HHSearch hit.

Convert a batch of 3D rotations [R] to quaternions [Q] R [...,3,3] Q [...,4]

Aligns template from the mmcif_object to the query. In case PDB70 contains a different version of the template sequence, we need to perform a

Removes chains that correspond to a single amino acid. A single amino acid in a chain is both N and C terminus. There is no force template fo

Removes the residues that Pdbfixer considers to be heterogens. Args: fixer: A Pdbfixer instance. alterations_info: A dict that will s

Replace the Se in any MET residues that were not marked as modified.

Runs the minimization pipeline. Args: pdb_string: A pdb string. max_iterations: An `int` specifying the maximum number of L-BFGS iter

Master function for setting up the lookup tables. These can either be loaded from a npz cache file or computed on the fly. Lookup tab

Makes sure that Var(W) = 1 and E[W] = 0

Superimposes coordinates onto a reference by minimizing RMSD using SVD. Args: reference: [N, 3] referenc

Converts sequences to an a3m file.

Aligns the sequences and returns the alignment in A3M string. Args: sequences: A list of query sequence strings. The sequences have

Compute rotation angles (as well as their sines and cosines) encoded by rotation matrices. Uses atan2 for better numerical stability for smal

Applies a Rotation -> Rotation function to the stored rotation object. Args: fn: A function of t

Flat-bottom loss to penalize structural violations between residues. This is a loss penalizing any violation of the geometry around the peptide

Loss to penalize steric clashes between residues. This is a loss penalizing any steric clashes due to non bonded atoms in different peptides

Computes the vector field Log_{mat_t}(mat_1). Args: mat_t (torch.Tensor): base point to compute vector field at. mat_1 (torc

calculate_igso3 pre-computes numerical approximations to the IGSO3 cdfs and score norms and expected squared score norms. Args: num_t

Composes the current rigid object with another. Args: r: Another Rigid object

Computes aligned confidence metrics from logits. Args: logits: [*, num_res, num_res, num_bins] the logits output from PredictedAlig

Find optimal renaming of ground truth based on the predicted positions. Alg. 26 "renameSymmetricGroundTruthAtoms" This renamed ground t

Compute several metrics to assess the structural violations.

Performs a nested concatenation of feature dicts. Args: np_dicts: list of dicts with the same structure. Each dict must have

Graph-conditioned sequence model

Creates Scatter3D objects for use in plotly. Args: pos_3d: [N, 3] array containing N points with euclidean coordinates.

Crop randomly to `crop_size`, or keep as is if shorter than that.

Delete the cache file.

IGSO(3) density. Args: expansion: truncated approximation of the power series in the IGSO(3) density. omega: length of an

Compute diffusion coefficient (g_t).

Sample based on length. Args: sample_length: length to sample Returns: Sample outputs.

Compute the derivative of the IGSO(3) angle probability distribution function with respect to the angles for pairs of angles and std dev leve

Input pipeline data transformers that can be ensembled and averaged.

Function for generating the angle probability distribution. Should return a 2D tensor with values for the std dev at the first dimens

Counts residues whose Ca is a large distance from its neighbour. Measures the fraction of CA-CA pairs between consecutive amino acids that are

Analyzes a protein and returns structural violation information. Args: prot_np: A protein. Returns: violations: A `dict` of stru

Generate a lookup table for the IGSO(3) probability distribution function of angles. Args: omega_grid: Grid of angle values ranging

Returns atom indices needed to compute chi angles for all residue types. Returns: A tensor of shape [residue_types=21, chis=4, atoms=4]. Th

Returns atom indices needed to compute chi angles for all residue types. Returns: A tensor of shape [residue_types=21, chis=4, atoms=4]. Th