Remove coords from MoleculeSetups in Meeko

[psharma-sr]

Evaluate if coords can be eliminated from MoleculeSetups and remove them if possible.

[diogomart]

@mallanos and @mattholc weren't as enthusiastic about this as me and @nbruciaferri, so we decided to not separate the coordinates from the molsetups, unless it really is necessary to address #131

[diogomart]

Arguments in favor of separating coords from molsetups:

• similarity to the design of openmm (topology and positions are separate) and RDKit (conformer objects are option in molecule objects)
• docking results are small trajectories
• could parameterize molecules without calculating their 3D coordinates

Against:

• not enough use cases for coord-less (pun not intended) molsetups to justify the risk of API user mistakes when molsetup and coords can be manipulated separately
• the positions of CG/G pseudo atom and generally offsite atoms depend on the positions of other atoms, even though this already partially mitigated because calculating the positions of offsite atoms is a two step process and the first step does not depend on coordinates.