Assess and design new structure for src

[luque82]

The src folder now includes a pyCapsid folder and a structure following the standard bin/ src/ ...

Check with Colin to determine the main parts, and then make a plan with the lab to refactor the code towards more flexible object-oriented programming that facilitates the addition of new tools.

In the future the current functionality of pyCapsid should be a specific module (for example, quasi-rigid domains or QRD). pyCapsid would include other functionalities, for example, assembly.