RNA second structure regexp pattern for HTML5 - regex

Question

I need a RegExp to identify RNA Second structure in an HTML5 web page.
An RNA Second Structure is simply a string that contains ONLY dot points and balancing parentheses and it's used to identify the RNA shape and if we know the target RNA shape we could guess the sequence of bases that could make an RNA with that target shape.
Please note it should contains at least One dot ..
For example
.....((((...).))..)....
(((....)))
....(((..)))...()...(....((..)))
are true RNA Second Structures but
.....((((....)))...
....a.((((......))))......
((((()))))
are not true structures
These are all my failed attempts to identifying structures:
<input type="text" pattern="/[.()]/g" />
<input type="text" pattern="/[.()]/g" />
<input type="text" pattern="/[\.\(\)]/g" />
<input type="text" pattern="/[().]/g" />
<input type="text" pattern="/[()\.]/g" />
<input type="text" pattern="/[\.()]/g" />
I'm new to RegExp and I should publish my program in the web because my teacher ordered me to do so!
And PLEASE just tell me the RegExp I should use! My program ( libRNA ) itself checks the balancing of parentheses!
libRNA

Answer 1

It is impossible to do generalized bracket balancing (finitely many nesting levels of brackets) with the level of support of JavaScript RegExp. (In Perl, PCRE, .NET regular expression, it is possible to do generalized bracket balancing).
You can write a simple JavaScript function to check, though:
function isValidSequence(str) {
if (!/\./.test(str)) {
// Dot . not found
return false;
}
var openBrackets = 0;
for (var i = 0; i < str.length; i++) {
if (str[i] === "(") {
openBrackets++;
} else if (str[i] === ")") {
if (openBrackets > 0) {
openBrackets--;
} else {
// Reject the case ..)(..
return false;
}
} else if (str[i] !== ".") {
// Garbage character, since it is not . or ( or )
return false;
}
}
// Check all brackets are properly closed
return openBrackets === 0;
}

Answer 2

/[().]+/g
would match everything that looks like an RNA Second Structure (i. e. a continuous sequence of dots and parentheses). You should first use this regex to find possible matches.
Then, you can check whether at least one dot is contained within each of those matches using
if (submatch.indexof(".") != -1)
But you can't check whether the parentheses are correctly balanced - for that you need a parser like nhahtdh suggested.

Answer 3

The problem here is that what you actually need to match is:
a = . | .(a) | (a). | .a | a.
The main problem why solving this with regular expressions will be hard if not impossible is that for every opening paranthesis there has to be a closing one.
It should be possible to do this with JavaScript. You need to do something like this:
Set paranthesis counter to 0. Iterate over the entire structure. When an opening paranthesis is found, increase counter. If you find a closing parenthesis, decrease the counter.
If at the end of the parsing the counter is back to zero, the structure is ok. Only thing missing now is the required dot. For that I would introduce another variable justOpened or something similar. When you find an opening paranthesis you set it to true. When you find a dot you set it to false. If you find a closing parenthesis and your variable is true you can abort, because your structure is broken.