I think my roommate is hot
Is that the only thing about her than you like?
No, I also think she's smart
Well there's nothing wrong with thinking your roommate is hot. Just don't make it weird for her and start hitting on her or something. That could cause a lot of problems you really don't want to deal with.
What, you think that is bad?
It depends on if she's receptive to it or not.  If she shuts you down, then forget it!  It'll make things really weird if you keep trying after she rejects you.