e364579d5fe914d7dc410b4e568b216ad0928cc1,src/biotite/structure/basepairs.py,,_get_proximate_basepair_candidates,#Any#Any#Any#,19

Before Change

        for candidate in candidates:
            partner_id = [array[int(candidate)].res_id,
                        array[int(candidate)].chain_id]
            if ( (distance(
                        array[int(candidate)].coord, atom.coord) > min_cutoff
                        ) 
                 & ((partner_id + atom_id) not in basepair_candidates)
            ):
                
                basepair_candidates.append(atom_id + partner_id)
    
    return basepair_candidates

After Change

    
    basepair_candidates = []
    
    for ix,iy in np.ndindex(adjacency_matrix.shape):
        if (adjacency_matrix[ix][iy]):
            candidate = [array[ix].res_id, array[ix].chain_id]
            partner = [array[iy].res_id, array[iy].chain_id]
            if ((distance(array[ix].coord, array[iy].coord) > min_cutoff) 
                 & ((partner + candidate) not in basepair_candidates)):
                
                basepair_candidates.append(candidate + partner)
    
    return basepair_candidates


        

Instances