38159553bea31a492f5a4716a223c3e774086501,src/biotite/structure/basepairs.py,,_get_proximate_basepair_candidates,#Any#Any#,1041

Before Change

            )
            // If the basepair candidate is not already in the output
            // list, append to the output list
            if (
                ((partner_res_start, candidate_res_start) \
                not in basepair_candidates)
                and ((candidate_res_start, partner_res_start) \
                not in basepair_candidates)
                and not (candidate_res_start == partner_res_start)
            ):
                basepair_candidates.append(
                    (candidate_res_start, partner_res_start)
                )
    return basepair_candidates


def _filter_atom_type(atom_array, atom_names):

After Change

    // indices.
    basepair_candidates = np.array(basepair_candidates)
    basepair_candidates_shape = basepair_candidates.shape
    basepair_candidates = get_residue_starts_for(
        atom_array, basepair_candidates.flatten()
    ).reshape(basepair_candidates_shape)

    // Remove candidates where the N/O pairs are from the same residue
    basepair_candidates = np.delete(
        basepair_candidates, np.where(
            basepair_candidates[:,0] == basepair_candidates[:,1]
        ), axis=0
    )
    // Sort the residue starts for each potential basepair
    for i, candidate in enumerate(basepair_candidates):
        basepair_candidates[i] = sorted(candidate)
    // Make sure each base pair candidate is only listed once

Instances