io

infill_chain_idx(chain_idx)

Infill the chain index tensor to fill in the gaps.

pdb_to_xyz(filename)

Parse a PDB file and return a tensor containing 3D coordinates of atoms.

Parameters:

Name	Type	Description	Default
filename	str	Path to a PDB file.	required

Returns:

Name	Type	Description
atom_xyz	torch.Tensor	A xyz coordinate tensor. Shape (n_residues, MAX_N_ATOMS_PER_RESIDUE, 3).
atom_mask	torch.BoolTensor	A mask tensor. 1 if the corresponding atom exists, 0 otherwise. Shape (n_residues, MAX_N_ATOMS_PER_RESIDUE)
chain_idx	torch.LongTensor	A LongTensor containing chain indices per residue. Shape (n_residues,)
chain_ids	List[str]	A list of unique chain IDs in the order of integers appearing in the chain_idx tensor.
seq	Dict[str, str]	A dictionary mapping chain IDs to amino acid sequences.

Note

MAX_N_ATOMS_PER_RESIDUE is set to 15 by default.

to_pdb(filename, coords, sequences, chain_ids, atoms=['N', 'CA', 'C', 'O', 'CB'])

Save coordinates to a PDB file.

Parameters:

Name	Type	Description	Default
filename	str	Path to the output PDB file.	required
coords	np.array	Coordinates of shape (5, L, 3), where the first dimension denotes the atom type.	required
atoms	List	Defaults to ["N", "CA", "C", "O", "CB"].	['N', 'CA', 'C', 'O', 'CB']