make sure self-links are applied

[fgrunewald]

In this PR we add molecule.interactions dict to the temporary dict in applied links. With that also interactions within a residue can be modified if need be. Also we add the option to remove nodes with the '{'replace':'atomname': null}' syntax as is the case for the vermouth applied links.

[fgrunewald]

problem with the current node removal is that it involves looping, copying and modifying the large interactions dict. So you wouldn't want to remove too many nodes. For now this is fine as it get's fix with vermouth adopting the clever interactions dict strategy.

[fgrunewald]

we need to do some bench marking before merging this