Datasets
Models
81 lines (65 with data), 3.0 kB
API Reference
Core Functions
Customization Functions
The SELFIES grammar is derived dynamically from a set of semantic constraints, which assign bonding capacities to various atoms. By default, :mod:`selfies` operates under the following constraints:
| Max Bonds | Atom(s) |
|---|---|
| 1 | F, Cl, Br, I |
| 2 | O |
| 3 | B, N |
| 4 | C |
| 5 | P |
| 6 | S |
| 8 | All other atoms |
The +1 and -1 charged versions of O, N, C, S, and P are also constrained, where a +1 increases the bonding capacity of the neutral atom by 1, and a -1 decreases the bonding capacity of the neutral atom by 1. For example, N+1 has a bonding capacity of 3 + 1 = 4, and N-1 has a bonding capacity of 3 − 1 = 2. The charged versions B+1 and B-1 are constrained to a capacity of 2 and 4 bonds, respectively.
However, the default constraints are inadequate for SMILES strings 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 strings cannot be represented by SELFIES strings 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 strings may be translated differently under different semantic constraints. Therefore, if custom semantic constraints are used, it is recommended to report them for reproducibility reasons.