Remove possibly unnecessary attributes in Atom class, and add_atom method

[diogomart]

Here are some things for consideration:

is_dummy and is_pseudo are redundant
#109 (comment)

we should probably ensure that the index of the atom in the MoleculeSetup.atoms list matches Atom.index, then we should have MoleculeSetup.add_atom behave like push in other languages: it appends to the end, and we remove options index and overwrite from add_atom.

The following should probably be removed:

Atom.graph
Atom.interaction_vectors
Atom.is_dummy