Improve the mapping operator

[jennyfothergill]

From a conversation with @chrisjonesBSU

chris:

Both backmap and CG_compound use some kind of mapping scheme, but it's formatted differently for each module. backmap takes a dictionary of {bead: smiles} but CG_compound takes a list of [bead, SMARTS]. I think it would be great if the same format was used in both. In this case, I think a dictionary would be best.

me:

great point! the mapping operators are not what I want them to be yet. 🤔 Basically I want a CG_Compound to be able to be created using SMARTS or a mapping operator. The mapping operator would be solely based on particle indices and would be saved as an attribute to the CG_Compound when the compound is created from SMARTS. Allowing a CG_Compound to be created from a mapping operator would be helpful for using it on simulation outputs that are not in optimal conformations. e.g., We can get the mapping from the initial frame (ideal positions--recognizable to smarts matching) using smarts and use the mapping on the last frame (maybe weird conformation). Another update I want to make is that we keep track of the anchors and bonds in the CG_Compound as they’re created so that no mapping is necessary to the backmap function. For instance, the only arg to backmap would be the CG compound!

[jennyfothergill]

fixed by #9