Replace type based connectivity with index based connectivity

[Lun4m]

Basically get rid networkx and use some sort of itp file.
@xinmeng2020 has the tools to set up writing all the info to the input h5 file, but it will be time consuming anyway.

This will allow for a better handiling of bonded interactions with the possibility of using different bonds, angles, etc for the same particle type.
It's important for cyclic groups, where you have to define different types for the atoms in cycle, and especially improper dihedrals because the atoms involved cannot be derived from a shortest path algorithm (I have to write a function myself to derive all paths of given length from one node).

[Lun4m]

Implemented but missing documentation.