Selfies

Added:
* Support for aromatic Te and triple bonds.
* Inbuild SELFIES to 1hot encoding, and 1hot encoding to SELFIES

Changed:
* Added default semantic constraints for charged atoms (single positive/negative charge of `[C]`, `[N]`, `[O]`, `[S]`, `[P]`)
* Raised the bond capacity of `P` to 7 bonds (from 5 bonds).

Bug Fixes:
* Fixed bug: `selfies.decoder` did not terminate for malformed SELFIES
that are missing the closed bracket `']'`.

---

Changed:
* Code so that is compatible with python >= 3.5.
* More descriptive error messages.

Bug Fixes:
* Minor bug fixes in the encoder for SMILES ending in branches (e.g. `C(Cl)(F)`),
and SMILES with ring numbers between branches (e.g. `C(Cl)1(Br)CCCC1`)
* Minor bug fix with ring ordering in decoder (e.g. `C1CC2CCC12` vs `C1CC2CCC21`).

---

Added:
* Added semantic handling of aromaticity / delocalization (by kekulizing SMILES with aromatic symbols before
they are translated into SELFIES by `selfies.encoder`).
* Added semantic handling of charged species (e.g. `[CH+]1CCC1`).
* Added semantic handling of radical species (`[CH]1CCC1`) or any species with explicit hydrogens (e.g. `CC[CH2]`).
* Added semantic handling of isotopes (e.g. `[14CH2]=C` or `[235U]`).
* Improved semantic handling of explicit atom symbols in square brackets, e.g. Carbene (`[C]=C`).
* Improved semantic handling of chirality (e.g. `O=C[Co](F)(Cl)(Br)(I)S`).
* Improved semantic handling of double-bond configuration (e.g. `F/C=C/C=C/C`).
* Added new functions to the library, such as `selfies.len_selfies` and
`selfies.split_selfies`.
* Added advanced-user functions to the library to customize the SELFIES semantic constraints, e.g.
`selfies.set_semantic_constraints`. Allows to encode for instance diborane, `[BH2]1[H][BH2][H]1`.
* Introduced new padding `[nop]` (no operation) symbol.

Changed:
* Optimized the indexing alphabet (it is base-16 now).
* Optimized the behaviours of rings and branches to fix an issue with specific non-standard molecules that could not be translated.
* Changed behaviour of Ring/Branch, such that states `X9991-X9993` are not necessary anymore.
* Significantly improved encoding and decoding algorithms, it is much faster now.

---

Added:
* Function ``get_alphabet()`` which returns a list of 29 selfies symbols
whose arbitrary combination produce >99.99% valid molecules.

Bug Fixes:
* Fixed bug which happens when three rings start at one node, and two of
them form a double ring.
* Enabled rings with sizes of up to 8000 SELFIES symbols.
* Bug fix for tiny ring to RDKit syntax conversion, spanning multiple
branches.

We thank Kevin Ryan (LeanAndMeangithub), Theophile Gaudin and Andrew Brereton
for suggestions and bug reports.

---

Added:
* Enabled ``[C],[CH],[C],[CH],[H]`` to use in a semantic
constrained way.

We thank Andrew Brereton for suggestions and bug reports.

---

Added:
* Decoder: added optional argument to restrict nitrogen to 3 bonds.
``decoder(...,N_restrict=False)`` to allow for more bonds;
standard: ``N_restrict=True``.
* Decoder: added optional argument make ring-function bi-local
(i.e. confirms bond number at target).
``decoder(...,bilocal_ring_function=False)`` to not allow bi-local ring
function; standard: ``bilocal_ring_function=True``. The bi-local ring
function will allow validity of >99.99% of random molecules.
* Decoder: made double-bond ring RDKit syntax conform.
* Decoder: added state X5 and X6 for having five and six bonds free.

Bug Fixes:
* Decoder + Encoder: allowing for explicit brackets for organic atoms, for
instance ``[I]``.
* Encoder: explicit single/double bond for non-canonical SMILES input
issue fixed.
* Decoder: bug fix for ``[Branch*]`` in state X1.

We thank Benjamin Sanchez-Lengeling, Theophile Gaudin and Zhenpeng Yao
for suggestions and bug reports.

---