Query single-straned and bulge region from given dot-bracket format

dot_bracket.py

def parse_dot_bracket_format(dot):
    binding_dict = {}
    for i, j in enumerate(dot):
        binding_dict[i] = None

    stack = []
    for i, j in enumerate(dot):
        if j == "(":
            stack.append(i)
        elif j == ")":
            bp1 = stack.pop()
            bp2 = i
            binding_dict[bp1] = bp2
            binding_dict[bp2] = bp1

    loops = []
    p = re.compile('[(][.]{1,1000}[)]')
    for m in p.finditer(dot):
        loops.append(m.span())

    stem_loops = []
    minor_space = []
    for loop in loops:
        i = loop[1] -1
        while True:
            if (i < len(dot)) and (dot[i] == ")") and not ((i - binding_dict[i] < 0)):
                last_valid = i
            if i > len(dot)-1:
                stem_loops.append([binding_dict[last_valid], last_valid])
                break
            if binding_dict[i] == None:
                i += 1
                continue
            if (i - binding_dict[i] < 0) or (binding_dict[i] in minor_space):
                stem_loops.append([binding_dict[last_valid], last_valid])
                break
            else:
                i += 1

    strand = []
    a = re.compile('[.]{1,1000}')
    dot_iter = a.finditer(dot)
    for m in dot_iter:
        strand.append(m.span())

    ss_strand = []
    bulge = []
    for d in strand:
        left = d[0]
        right = d[1]
        if (left == 0) or (right > len(dot)-1):
            ss_strand.append((left, right-1))
            continue
        if (dot[left-1] == ')' and dot[right] == '('):
            ss_strand.append((left, right-1))
            continue
        if ((dot[left-1] == ')' and dot[right] == ')') or (dot[left-1] == '(' and dot[right] == '(')):
            bulge.append((left, right-1))
    return ss_strand, bulge