File formats

[ppxasjsm]

One of the first things that should be decided upon, is the kind of input and output file formats that will eventually be supported here.

A related discussion we should probably take into account can be found on alchemsitry.org github page:
https://github.com/alchemistry/fileformat

[jchodera]

To be specific, each stage of the setup pipeline will consist of a small component that consumes and produces a file or object (or group of files/objects) that specifies:

• the topology (atomic elements, connectivity, and likely bond orders) of polymers, small molecules, ions, etc.
• the atomic positions for some or all of the atoms
• potentially, parameters assigned to some or all of the molecules/residues