Code:
for line in lines:
    line_number = line_number + 1
    if line[0] == " ":
        found_it = 0
        cindex = 0
        while cindex < len(linked_types) and found_it != 0:
            if linked_types[cindex] in line:
                found_it = 1
            cindex=cindex+1
A while loop is not designed to iterate through a list, while a for loop is. This is because a while loop is designed to continue going until certain conditions are met. Thus, you must do things manually. You could also do:
Code:
for line in lines:
    line_number = line_number + 1
    if line[0] == " ":
        found_it = 0
        cindex = 0
        lt2=linked_types[:]
        while len(lt2) and found_it != 0:
            types=lt2.pop()
            if types in line:
                found_it = 1
            cindex=cindex+1
Still, the best way of all is:
Code:
print "\nChecking the link types:"
line_number
for line in lines:
    if line[0] == " ":
        found_it = 0
        for types in link_types:
            if types in line:
                found_it = 1
                break
        if found_it == 0:
            print line
When iterating through a list, use a For loop. Its designed for it. Just use the break statement to break out of it when you so desire.