Question regarding security deposit and carpets

[Dianna Marble]

Hello,

I recently had tenants move out of a rental unit. When they moved in, the carpets were brand new, and they only lived there 6 months. While inspecting the home, we smelled extreme odor of pet urine through out the house. We had the carpet professionally cleaned the day after they moved out and the smell was still there. (The carpet cleaning guy even remarked how strong the odor was.) We had a contractor come in to assess the carpets and when he took them up, he said they were dripping with urine (and almost made him puke). All the carpets smelled but the living room and master bedroom were the worst smelling. When all the carpets were removed, the living room had major urine damage done to the hardwood floors and part of the master bedroom floor had to be completely replaced. The other 2 bedroom floors were not damaged but the carpets smelled of urine.
One of the tenants has contacted us asking when they will receive their security deposit back. 
It is in their rental agreement contract that they must keep all carpets free of odor and that the house must be returned in the same condition as when they moved in.
My questions are:
Can we charge them for us having to have the carpets professionally cleaned even though it did not remove the odor?
Can we put their security deposit towards replacing the floor and carpets?
Can we bill them for what their deposit didn't cover?
Can we charge them for labor for us personally replacing the floor and for the time it took to remove the odor from the living room floors?

We have 'before' pictures of the carpets from when we were advertising to rent the house and we have many 'after' pictures of the carpets and floors that were ruined.

Thank you in advance.