Toff

Added

- `toff.utils.generate_structure`. this function can now be used to also take parameters from GAFF and/or Espaloma. For that openmmforcefields must be installed.
In the case of Espaloma, this module has to be installed as well.

Changed

- Now the default force field in the class `toff.utils.Parameterize` is selected base on the keyword `force_field_type`. They are:
- openff -> openff_unconstrained-2.0.0.offxml
- gaff -> gaff-2.11
- espaloma -> espaloma-0.2.2

Added

- `toff.utils.get_rdkit_mol` accept `sdf` molecules too. Only the first molecule/conformer will be used.
- Example using the `safe_naming_prefix` on `toff.utils.Parameterize`.

Changed

- `toff.utils.confgen` now check if it is needed to generate a conformation and add hydrogens.

Removed

- Parameter `gen_conformer` from `toff.utils.get_rdkit_mol` and `toff.utils.parameterize.__call__`.

Added

- `toff.utils.safe_naming`. Add a prefix to the atom types.
- `safe_naming_prefix` keyword on `toff.utils.Parameterize`. It uses the previous function if some string is provided.
- `max_iter` to `toff.utils.charge_sanitizer`. Maximum number of iteration in case of charge correction.

Fixed

- Improve documentation

Pre-release