b23057850bf29e34add32c76b6b59550825e82a3,src/biotite/structure/basepairs.py,,_get_std_thymine,#,169

Before Change

    // Create boolean masks for the AtomArray containing the bases` 
    // heteroatoms which (or the usually attached hydrogens) can act as
    // Hydrogen Bond Donors or Acceptors respectively.
    hbond_donors = np.zeros(10, dtype=bool)
    hbond_d = [1, 4]
    hbond_donors[hbond_d] = np.ones(len(hbond_d), dtype=bool)
    
    hbond_acceptors = np.zeros(10, dtype=bool)
    hbond_a = [1, 3, 4, 6]
    hbond_acceptors[hbond_a] = np.ones(len(hbond_a), dtype=bool)

    return [thymine, thymine_pdbv3], [pyrimidine_center], \
           [hbond_donors, hbond_acceptors]


def _get_std_uracil():
    atom1 = Atom([-2.481, 5.354, 0.000], atom_name="C1*", res_name="U")

After Change

    // Create boolean masks for the AtomArray containing the bases` 
    // heteroatoms which (or the usually attached hydrogens) can act as
    // Hydrogen Bond Donors or Acceptors respectively.
    hbond_donor_mask = _get_1d_boolean_mask(
        thymine_pdbv2.array_length(), [1, 4]
                                        )
    hbond_acceptor_mask = _get_1d_boolean_mask(
        thymine_pdbv2.array_length(), [1, 3, 4, 6]
                                            )
      
    return [thymine_pdbv2, thymine_pdbv3], [pyrimidine_center], \
           [hbond_donor_mask, hbond_acceptor_mask]


def _get_std_uracil():
    atom1 = Atom([-2.481, 5.354, 0.000], atom_name="C1*", res_name="U")

Instances