def chain_to_coords()

in data/prepare_GO_data.py [0:0]

• 22 lines of code
• 7 McCabe index (conditional complexity)

def chain_to_coords(chain, target_atoms=["N", "CA", "C", "O"], name=""):
    """Convert a PDB chain in to coordinates of target atoms from all
    AAs

    Args:
        chain: a Bio.PDB.Chain object
        target_atoms: Target atoms which residues will be resturned.
        name: String. Name of the protein.
    Returns:
        Dictonary containing protein sequence `seq`, 3D coordinates `coord` and name `name`.

    """
    output = {}
    # get AA sequence in the pdb structure
    pdb_seq = "".join(
        [
            three_to_one_standard(res.get_resname())
            for res in chain.get_residues()
            if is_aa(res)
        ]
    )
    if len(pdb_seq) <= 1:
        # has no or only 1 AA in the chain
        return None
    output["seq"] = pdb_seq
    # get the atom coords
    coords = np.asarray(
        [
            get_atom_coords(res, target_atoms=target_atoms)
            for res in chain.get_residues()
            if is_aa(res)
        ]
    )
    output["coords"] = coords.tolist()
    output["name"] = "{}-{}".format(name, chain.id)
    return output