update ONIOM and TAtomList

[Albkat]

1. add warning if the distances between added link atom (H) and any other atom is too short (smaller than H2) -> check_dist

2. update man page

3. allow for 0 in TAtomList (e.g. 1,2,0,12)

[awvwgk]

Why do we need zeros in the atom list, this sounds like some out of bounds issue to me.

[Albkat]

Why do we need zeros in the atom list, this sounds like some out of bounds issue to me.

So, the problem right now is that zeros in Atomlist will throw segfault. Alternatively, we could raise an error.

[awvwgk]

I think we should rather add checks to avoid adding zeros in the first place to the list.

[Albkat]

I think we should rather add checks to avoid adding zeros in the first place to the list.

I assume that performing a direct check is not possible since the TAtomList parser is explicitly composed of pure procedures. I've altered the error handling approach: now, whenever it encounters a non-integer value or zero, it throws an error. If you have any more insightful suggestions for enhancing this, I'd be glad to hear them.

[awvwgk]

Looks good to me then