990cab8e4e0aa424e9ab506966efc9642a682015,src/biotite/structure/basepairs.py,,_get_std_adenine,#,54

Before Change

        [atom1, atom2, atom3, atom4, atom5, atom6, atom7, atom8,
         atom9, atom10, atom11]
    )
    adenine_pdbv3 = adenine_pdbv2.copy()
    adenine_pdbv3.atom_name[[0]] = ["C1""]

    // Get the midpoint between the N1 and C4 atoms
    midpoint = np.mean([atom8.coord, atom11.coord], axis=-2)
    // Calculate the coordinates of the aromatic ring centers
    pyrimidine_center = np.mean(
        [atom5.coord, atom6.coord, atom8.coord,
         atom9.coord, atom10.coord, atom11.coord], axis=-2
    )
    imidazole_center = np.mean(
        [atom2.coord, atom3.coord, atom4.coord,
         atom5.coord, atom11.coord], axis=-2
    )

    // Create boolean masks for the AtomArray containing the bases`
    // heteroatoms (or the usually attached hydrogens) which can act as
    // Hydrogen Bond Donors or Acceptors respectively.
    hbond_donor_mask = _get_1d_boolean_mask(
        adenine_pdbv2.array_length(), [1, 6]
    )
    hbond_acceptor_mask = _get_1d_boolean_mask(
        adenine_pdbv2.array_length(), [1, 3, 6, 7, 9]
    )

    return (adenine_pdbv2, adenine_pdbv3), \
           (midpoint, pyrimidine_center, imidazole_center), \
           (hbond_donor_mask, hbond_acceptor_mask)

After Change

         atom5.coord, atom11.coord], axis=-2
    )

    return adenine, (midpoint, pyrimidine_center, imidazole_center)


def _get_std_cytosine():
    

Instances