bakery: reverse mapping tool v3.0

Modified the prepare_files.py code to allow two-step processing. In the first step the system graph with the selected appropriate atomistic fragment is built and saved. Next, with an external tool (see examples/network_backmapping/abx/scan_bonds.py) the actual list of active sites for atomistic cross bonds can be prepared and included into the settings file (tag predefined_active_sites) for the next step.
The last step uses the predefined active sites to build the hybrid topology file.

bakery: reverse mapping tool v2.0

Updated version of generic reverse mapping method for complex polymer systems.

bakery: reverse mapping tool v1.3

The extended version of bakery tool with additional examples of trimethylol-melamine and the polyethylene case with higher degree of coarse-graining.

bakery: reverse mapping tool v1.2

New examples, trimethylol melamine and polyethylene (coarse-graining level 10->1)

bakery: reverse mapping tool v1.1

The set of tools to perform reverse mapping operation, from coarse-graining state to fine-grain.

bakery: reverse mapping tool

The latest version of bakery tool with updated examples.