Support for two energy terms of the same type per State

[jakublala]

As pointed out by @arnav-cheruku, currently we do not support having two energy terms of the same type on the State, as they will get overwritten in the dictionary that keeps track of the value:

bagel/src/bagel/state.py

Line 54 in 3f05441

_energy_terms_value: dict[(str, float)] = field(default_factory=lambda: {}, init=False)

We should fix this by either making the dictionary take the actual energy term as the key; or have unique identifiers.

Moreover, we should support custom names for the terms, or have some sort of a clear differentiator of different terms of the same type, so that the logging also works properly. This has not been a problem - for instance - for the pLDDT term given that we also have an OverallPLDDT term that has made this bug hard to see.

[jakublala]

@sangioletti This issue made me realize that it might be valuable to create StateEnergy or Energy class, that stores the list of energy terms, and their values as well. It takes as input the oracles output - it would remove some of the complexity / logic from State, and avoid having both an energy term list, and energy term values list - as attributes of the State class, which might make it a bit confusing.

Likely a low priority, we will sort it out otherwise for now for v0.1; but for v0.2 potentially.

Let me knoe your thoughts.

[jakublala]

This has been hotfixed in #68, but keeping it here for reference for a proper fix and feature update.