Compute absolute difference between two angles.

Apply inverse Rigid3Array transform to point.

Applies inverse Rot3Array to point.

Applies the `operations` in right-to-left order.

Converts batch object to dictionary.

Checks whether two Structure objects could be considered equal. Args: struc1: First Structure object. struc2: Second Structure object

Mapping to per-atom features and self-attention on subsets.

Cross-attention on flat atom subsets and mapping to per-token features.

Gets a list of atom ID tuples from Structure class arrays. Returns: A list of tuples of (chain_id, res_id, insertion_code, atom_name) where

Extract AtomLayout from a Structure.

Atoms table.

Marks a field as having a default factory derived from its type.

Ensures that a bfloat16 parameter is provided by casting if necessary.

Bonds table.

Builds intermediate data.

Returns the chain auth asym ID for each atom in the structure.

The indices in the atom fields where each present chain begins.

Returns the entity description for each atom in the structure.

Returns the entity ID for each atom in the structure.

Compute predicted distance errors for all pairs of chains. Args: num_tokens: The number of tokens (not including padding). asym_ids: The as

Ordered internal chain IDs (label_asym_id) present in the Structure.

Chains table.

Checks if a binary exists on the given path and raises otherwise.

Returns the sizes of the MSA crop and MSA_all_seq crop. NOTE: Unpaired + paired MSA sizes can exceed total_msa_size when there are lots of gapp

Returns a cleaned version of the input structure. Args: struc: Structure to clean. ccd: The chemical components dictionary. drop_missin

The names of the columns in the table, including the key column.

Compares chirality of ligands in a structure with reference molecules. We do not enforce that ligand atoms exactly match, only that the ligand atom

Compute the template features.

Compute the per-token features.

Compute the PredictedStructureInfo features. Args: all_tokens: flat AtomLayout with 1 representative atom per token, shape (num_tok

Computes the InterChainBondInfo features. Args: all_tokens: AtomLayout for tokens; shape (num_tokens,). all_token_atoms_layout: Atom

Computes the InterChainBondInfo features. Args: all_tokens: AtomLayout for tokens; shape (num_tokens,). bond_layout: Bond layout for

Compute the PseudoBetaInfo features. Args: all_token_atoms_layout: AtomLayout for all atoms per token, shape (num_tokens, max_atom

Reference structure information for each residue.

Pads the all_token_atoms_layout and stores other data.

Computes gather indices and meta data to work with a flat atom list.

Computes features for backbone frames.

Concatenates the tables across a sequence of databases. Args: dbs: A non-empty sequence of database instances of the same type. Returns:

Concatenates bonds tables and atom keys simultaneously. Args: bonds_tables: A sequence of `Bonds` instances to concatenate. If any are No

Convert an array from one atom layout to another.

Converts MSA in the A3M format to the Stockholm format.

Converts MSA in Stockholm format to the A3M format.

A [..., num_atom, 3] shaped array of atom coordinates.

Returns a copy of this database with the specified changes applied.

Returns a copy with the x, y and z columns updated.

Like copy_and_update but changes are arrays of length num_residues. These changes are first scattered into arrays of length num_atoms such th

Returns a shallow copy with the residues table updated.

Make zero-coordinate structure from all physical residues. Args: struc: Structure object. ccd: The chemical components dictionary. with

Create and concatenate MSA features.

Creates per-chain MSA features where the MSAs have been aligned. Args: chains: A list of feature dicts, one for each chain. max_paired_sequ

Creates a fasta file with the sequence with line width limit.

Add relative position encodings.

Make target feat.

Deduplicates unpaired sequences based on paired sequences.

Computes torsion angle for a quadruple of points. For points (a, b, c, d), this is the angle between the planes defined by points (a, b, c) and (