1aa361f32c59fb5b3a7a9b54d12fdee3f35e2176,src/biotite/structure/basepairs.py,,_get_proximate_basepair_candidates,#Any#Any#Any#,814

Before Change

                break
            // Check if the basepair candidates have a distance which is
            // greater than the minimum cutoff
            if(distance(
                atom_array[candidate].coord, atom_array[partner].coord
                        ) > min_cutoff
            ): 
                // Find the indices of the first atom of the residues
                candidate_res_start = np.where(
                    (atom_array.res_id == atom_array[candidate].res_id)
                    & (atom_array.chain_id == atom_array[candidate].chain_id)
                                            )[0][0]
                partner_res_start = np.where(
                    (atom_array.res_id == atom_array[partner].res_id)
                    & (atom_array.chain_id == atom_array[partner].chain_id)
                                )[0][0]
                // If the countperpart of the basepair candidates is not
                // already in the output list, append to the output
                if (partner_res_start, candidate_res_start) \
                    not in basepair_candidates:
                    basepair_candidates.append(
                        (candidate_res_start, partner_res_start)
                                            )
    return basepair_candidates


def _filter_atom_type(atom_array, atom_names):

After Change

    // Get a boolean mask for the C1 sugar atoms
    NOmask = (filter_nucleotides(atom_array) 
              & np.isin(atom_array.element, ["N", "O"]))
    // Get the indices of the C1 atoms that are within the maximum cutoff
    // of each other
    indices = CellList( 

Instances