def get_atom_coords()

in data/prepare_GO_data.py [0:0]

• 9 lines of code
• 3 McCabe index (conditional complexity)

def get_atom_coords(residue, target_atoms=["N", "CA", "C", "O"]):
    """Extract the coordinates of the target_atoms from an AA residue.
    Handles exception where residue doesn't contain certain atoms
    by setting coordinates to np.nan

    Args:
        residue: a Bio.PDB.Residue object.
        target_atoms: Target atoms which residues will be resturned.

    Returns:
        np arrays with target atoms 3D coordinates in the order of target atoms.
    """
    atom_coords = []
    for atom in target_atoms:
        try:
            coord = residue[atom].coord
        except KeyError:
            coord = [np.nan] * 3
        atom_coords.append(coord)
    return np.asarray(atom_coords)