SMARTS patterns to guesstimate fragment charges

[cstein]

We should make an effort in using SMARTS patterns to guesstimate the fragment charges and only (ONLY!) use the charge model if there are things we are uncertain about.

In the long run, we should probably also dump some information to a json-file (which can be read back in) regarding charges and other things. Now, it will become incomprehensible for even the keenest of users, but it should and could be a nice option.

{
  "title": "This is a test",
  "charge": 0,
  "fragments": 4,
  "fragment_charges": [ 0, 0, 0, 0],
  "fragment_indices": [
    [ 1, 2, 3],
    [ 4, 5, 6],
    [ 7, 8, 9],
    [10,11,12]
  ],
  "fragment_names": [
    "WATER",
    "WATER",
    "WATER",
    "WATER"
  ]
}