Fix charged species

[shihchengli]

Motivation or Problem

The current fix module doesn't have remedies for charged species. This PR add a function to convert a radical species to charged species based on the added remedies (need to be extended).

Here are some examples:

1. [Cl] to [Cl-]

2. [C]#N to [C-]#N

3. methanethiolate

[xiaoruiDong]

Hi @shihchengli, thank you so much! These are good additions. Do you think it makes sense to add an argument for charge (int). Basically, it informs the algorithm about the formal charge of the molecule. Even if it doesn't have an effect at the moment, I hope we can include it as a place holder for future development. And can you merge it into the v1.0/dev branch? Where remedies and fix functions are decoupled. Thanks