Epic: Finish basepair implementation

[jrihon]

💡 Summary

In a work-in-progress branch, I had implemented basepairing capabilities. It is best to finish this feature and document it before refactoring the whole

🔎 Scope & Requirements

This epic would touch the following parts of the code :

• src/build
• docs

This needs to be finished in order for this epic to be considered done :

• The CLI is functional to the point all old functionalities are added to the main code
• Added to the docs
• Store asset files (like xyz, pdb files etc) under the correct directory for later

Linked Tasks / Features

• #IssueNumber