Add a mutation function which substitutes atoms.

[lukasturcani]

Add a mutation function which allows the user to specify a query molecule, which should match a single atom, and a replacement atom. The mutation function should substitute the atom matched by the query molecule with the one specified as an input.

The function should also take an optional sanitization function as a parameter. This function can perform any additional cleanup operations on the atom and molecule to make sure the valences are in order, for example.

[asantanabo]

I will be looking into