model/dataset/protein.py

import dataclasses
import numpy as np

from utils import residue_constants

PDB_CHAIN_IDS = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789'
PDB_MAX_CHAINS = len(PDB_CHAIN_IDS)


@dataclasses.dataclass(frozen=True)
class Protein:
    atom_positions: np.ndarray
    aatype: np.ndarray
    atom_mask: np.ndarray
    residue_index: np.ndarray
    chain_index: np.ndarray
    b_factors: np.ndarray

    def __post_init__(self):
        if len(np.unique(self.chain_index)) > PDB_MAX_CHAINS:
            raise ValueError(
                f'Cannot build an instance with more than {PDB_MAX_CHAINS}'
            )


def _chain_end(atom_index, end_resname, chain_name, residue_index) -> str:
    chain_end = 'TER'
    return (f'{chain_end:<6}{atom_index:>5}      {end_resname:>3} '
            f'{chain_name:>1}{residue_index:>4}')


def to_pdb(prot: Protein, model=1, add_end=True) -> str:
    """Converts a `Protein` instance to a PDB string.

  Args:
    prot: The protein to convert to PDB.

  Returns:
    PDB string.
  """
    restypes = residue_constants.restypes + ['X']
    res_1to3 = lambda r: residue_constants.restype_1to3.get(restypes[r], 'UNK')
    atom_types = residue_constants.atom_types

    pdb_lines = []

    atom_mask = prot.atom_mask
    aatype = prot.aatype
    atom_positions = prot.atom_positions
    residue_index = prot.residue_index.astype(int)
    chain_index = prot.chain_index.astype(int)
    b_factors = prot.b_factors

    if np.any(aatype > residue_constants.restype_num):
        raise ValueError('Invalid aatypes.')

    # Construct a mapping from chain integer indices to chain ID strings.
    chain_ids = {}
    for i in np.unique(chain_index):  # np.unique gives sorted output.
        if i >= PDB_MAX_CHAINS:
            raise ValueError(
                f'The PDB format supports at most {PDB_MAX_CHAINS} chains.')
        chain_ids[i] = PDB_CHAIN_IDS[i]

    pdb_lines.append(f'MODEL     {model}')
    atom_index = 1
    last_chain_index = chain_index[0]
    # Add all atom sites.
    for i in range(aatype.shape[0]):
        # Close the previous chain if in a multichain PDB.
        if last_chain_index != chain_index[i]:
            pdb_lines.append(_chain_end(
                atom_index, res_1to3(aatype[i - 1]), chain_ids[chain_index[i - 1]],
                residue_index[i - 1]))
            last_chain_index = chain_index[i]
            atom_index += 1  # Atom index increases at the TER symbol.

        res_name_3 = res_1to3(aatype[i])
        for atom_name, pos, mask, b_factor in zip(
                atom_types, atom_positions[i], atom_mask[i], b_factors[i]):
            if mask < 0.5:
                continue

            record_type = 'ATOM'
            name = atom_name if len(atom_name) == 4 else f' {atom_name}'
            alt_loc = ''
            insertion_code = ''
            occupancy = 1.00
            element = atom_name[0]  # Protein supports only C, N, O, S, this works.
            charge = ''
            # PDB is a columnar format, every space matters here!
            atom_line = (f'{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}'
                         f'{res_name_3:>3} {chain_ids[chain_index[i]]:>1}'
                         f'{residue_index[i]:>4}{insertion_code:>1}   '
                         f'{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}'
                         f'{occupancy:>6.2f}{b_factor:>6.2f}          '
                         f'{element:>2}{charge:>2}')
            pdb_lines.append(atom_line)
            atom_index += 1

    # Close the final chain.
    pdb_lines.append(_chain_end(atom_index, res_1to3(aatype[-1]),
                                chain_ids[chain_index[-1]], residue_index[-1]))
    pdb_lines.append('ENDMDL')
    if add_end:
        pdb_lines.append('END')

    # Pad all lines to 80 characters.
    pdb_lines = [line.ljust(80) for line in pdb_lines]
    return '\n'.join(pdb_lines) + '\n'  # Add terminating newline.