.. currentmodule:: selfies
.. autofunction:: encoder
.. autofunction:: decoder
.. autofunction:: len_selfies
.. autofunction:: split_selfies
.. autofunction:: get_alphabet_from_selfies
.. autofunction:: get_semantic_robust_alphabet
.. autofunction:: selfies_to_encoding
.. autofunction:: encoding_to_selfies
.. autofunction:: batch_selfies_to_flat_hot
.. autofunction:: batch_flat_hot_to_selfies
By default, :mod:`selfies` operates under the following semantic constraints
| Max Bonds | Atom(s) |
|---|---|
| 1 | F, Cl, Br, I |
| 2 | O |
| 3 | N |
| 4 | C |
| 5 | P |
| 6 | S |
| 8 | All other atoms |
The +1 and -1 charged versions of O, N, C, S, P are also constrained,
where a +1 increases the maximum bond capacity of the neutral atom by 1,
and a -1 decreases the maximum bond capacity of the neutral atom by 1.
For example, N+1 has a bond capacity of 3 + 1 = 4,
and N-1 has a bond capacity of 3 - 1 = 2.
However, the default constraints are inadequate for SMILES that violate them. For
example, nitrobenzene O=N(=O)C1=CC=CC=C1 has a nitrogen with 6 bonds and
the chlorate anion O=Cl(=O)[O-] has a chlorine with 5 bonds - these
SMILES cannot be represented as SELFIES under the default constraints.
Additionally, users may want to specify their own custom constraints. Thus, we
provide the following methods for configuring the semantic constraints
of :mod:`selfies`.
Warning
SELFIES may be translated differently under different semantic constraints. Therefore, if custom semantic constraints are used, it is recommended to report them for reproducibility reasons.
.. autofunction:: get_default_constraints
.. autofunction:: get_octet_rule_constraints
.. autofunction:: get_hypervalent_constraints
.. autofunction:: get_semantic_constraints
.. autofunction:: set_semantic_constraints