SELFIES Examples

import sys
sys.path.append('../')

import selfies as sf
from rdkit import Chem

Standard Usage

First let’s try translating from SMILES to SELFIES, and then from SELFIES to SMILES. We will use a non-fullerene acceptor for organic solar cells as an example.

smiles = "CN1C(=O)C2=C(c3cc4c(s3)-c3sc(-c5ncc(C#N)s5)cc3C43OCCO3)N(C)C(=O)" \
         "C2=C1c1cc2c(s1)-c1sc(-c3ncc(C#N)s3)cc1C21OCCO1"
encoded_selfies = sf.encoder(smiles)  # SMILES --> SEFLIES
decoded_smiles = sf.decoder(encoded_selfies)  # SELFIES --> SMILES

print(f"Original SMILES: {smiles}")
print(f"Translated SELFIES: {encoded_selfies}")
print(f"Translated SMILES: {decoded_smiles}")

Original SMILES: CN1C(=O)C2=C(c3cc4c(s3)-c3sc(-c5ncc(C#N)s5)cc3C43OCCO3)N(C)C(=O)C2=C1c1cc2c(s1)-c1sc(-c3ncc(C#N)s3)cc1C21OCCO1
Translated SELFIES: [C][N][C][Branch1_2][C][=O][C][=C][Branch2_1][Ring2][Branch1_3][C][=C][C][=C][Branch1_1][Ring2][S][Ring1][Branch1_1][C][S][C][Branch1_1][N][C][=N][C][=C][Branch1_1][Ring1][C][#N][S][Ring1][Branch1_3][=C][C][Expl=Ring1][N][C][Ring1][S][O][C][C][O][Ring1][Branch1_1][N][Branch1_1][C][C][C][Branch1_2][C][=O][C][Ring2][Ring1][=N][=C][Ring2][Ring1][P][C][=C][C][=C][Branch1_1][Ring2][S][Ring1][Branch1_1][C][S][C][Branch1_1][N][C][=N][C][=C][Branch1_1][Ring1][C][#N][S][Ring1][Branch1_3][=C][C][Expl=Ring1][N][C][Ring1][S][O][C][C][O][Ring1][Branch1_1]
Translated SMILES: CN7C(=O)C6=C(C1=CC4=C(S1)C=3SC(C2=NC=C(C#N)S2)=CC=3C45OCCO5)N(C)C(=O)C6=C7C8=CC%11=C(S8)C=%10SC(C9=NC=C(C#N)S9)=CC=%10C%11%12OCCO%12

When comparing the original and decoded SMILES, do not use == equality. Use RDKit to check whether both SMILES correspond to the same molecule.

print(f"== Equals: {smiles == decoded_smiles}")

# Recomended
can_smiles = Chem.CanonSmiles(smiles)
can_decoded_smiles = Chem.CanonSmiles(decoded_smiles)
print(f"RDKit Equals: {can_smiles == can_decoded_smiles}")

== Equals: False
RDKit Equals: True

Advanced Usage

Now let’s try to customize the SELFIES constraints. We will first look at the default SELFIES semantic constraints.

default_constraints = sf.get_semantic_constraints()
print(f"Default Constraints:\n {default_constraints}")

Default Constraints:
 {'H': 1, 'F': 1, 'Cl': 1, 'Br': 1, 'I': 1, 'O': 2, 'N': 3, 'C': 4, 'P': 5, 'S': 6, '?': 8}

We have two compounds here, CS=CC#S and [Li]=CC in SELFIES form. Under the default SELFIES settings, they are translated like so. Note that since Li is not recognized by SELFIES, it is constrained to 8 bonds by default.

c_s_compound = sf.encoder("CS=CC#S")
li_compound = sf.encoder("[Li]=CC")

print(f"CS=CC#S --> {sf.decoder(c_s_compound)}")
print(f"[Li]=CC --> {sf.decoder(li_compound)}")

CS=CC#S --> CS=CC#S
[Li]=CC --> [Li]=CC

We can add Li to the SELFIES constraints, and restrict it to 1 bond only. We can also restrict S to 2 bonds (instead of its default 6). After setting the new constraints, we can check to see if they were updated.

new_constraints = default_constraints
new_constraints['Li'] = 1
new_constraints['S'] = 2

sf.set_semantic_constraints(new_constraints)  # update constraints

print(f"Updated Constraints:\n {sf.get_semantic_constraints()}")

Updated Constraints:
 {'H': 1, 'F': 1, 'Cl': 1, 'Br': 1, 'I': 1, 'O': 2, 'N': 3, 'C': 4, 'P': 5, 'S': 2, '?': 8, 'Li': 1}

Under our new settings, our previous molecules are translated like so. Notice that our new semantic constraints are met.

print(f"CS=CC#S --> {sf.decoder(c_s_compound)}")
print(f"[Li]=CC --> {sf.decoder(li_compound)}")

CS=CC#S --> CSCC=S
[Li]=CC --> [Li]CC

To revert back to the default constraints, simply call:

sf.set_semantic_constraints()