1675e2873db77528ef1dee6fc49aaccfca9a369b,src/biotite/structure/dotbracket.py,,dot_bracket,#Any#Any#Any#,60

Before Change

    for s, solution in enumerate(pseudoknot_order):
        // Bases whose partners have an opened bracket
        opened_brackets = set()
        for pos in range(length):
            if pos not in basepairs:
                notations[s] += "."
            else:
                // Get position in ``basepairs`` and ``pseudoknot_order``
                bp_pos = np.where(basepairs == pos)[0][0]
                if pos in opened_brackets:
                    notations[s] += _CLOSING_BRACKETS[solution[bp_pos]]
                else:
                    for base in basepairs[bp_pos]:
                        if base != pos:
                            opened_brackets.add(base)
                    notations[s] += _OPENING_BRACKETS[solution[bp_pos]]

    return notations

def base_pairs_from_dot_bracket(dot_bracket_notation):
    

After Change

    // Each optimal pseudoknot order solution is represented in
    // dot-bracket-notation
    notations = [
        bytearray(("."*length).encode()) for _ in range(len(pseudoknot_order))
    ]
    for s, solution in enumerate(pseudoknot_order):
        for basepair, order in zip(basepairs, solution):
            notations[s][basepair[0]] = _OPENING_BRACKETS_BYTES[order]

Instances