enumerate-smiles

A Python library enumerating heterocycles, stereoisomers, tautomers and SMILES.

💪 Getting Started

from enumerate_smiles import SmilesEnumerator
from rdkit import Chem

smiles_list = [
  # erlotinib
  "n1cnc(c2cc(c(cc12)OCCOC)OCCOC)Nc1cc(ccc1)C#C",
  # midecamycin
  "CCC(=O)O[C@@H]1CC(=O)O[C@@H](C/C=C/C=C/[C@@H]([C@@H](C[C@@H]([C@@H]([C@H]1OC)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)C)O[C@H]3C[C@@]([C@H]([C@@H](O3)C)OC(=O)CC)(C)O)N(C)C)O)CC=O)C)O)C",
  # selenofolate
  "C1=CC(=CC=C1C(=O)NC(CCC(=O)OCC[Se]C#N)C(=O)O)NCC2=CN=C3C(=N2)C(=O)NC(=N3)N",
]
# Ensure hydrogens are explicit
mols = [Chem.AddHs(Chem.MolFromSmiles(smiles)) for smiles in smiles_list]

se = SmilesEnumerator()
print(se.enumerate(mols))

The above enumerates heterocycles, tautomers, resonance forms, stereoismers and SMILES.

Multiprocessing can be enabled by setting the njobs argument.

One may output the enumerated SMILES to a file as follows:

from enumerate_smiles import SmilesEnumerator
from io import StringIO

output = StringIO()

se = SmilesEnumerator()
se.enumerate_to_file(mols, output, njobs=5)

For convenience, users may use a MolSupplier instance instead of a list of molecules.

from enumerate_smiles import MolSupplier

input = StringIO("""n1cnc(c2cc(c(cc12)OCCOC)OCCOC)Nc1cc(ccc1)C#C   erlotinib
CCC(=O)O[C@@H]1CC(=O)O[C@@H](C/C=C/C=C/[C@@H]([C@@H](C[C@@H]([C@@H]([C@H]1OC)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)C)O[C@H]3C[C@@]([C@H]([C@@H](O3)C)OC(=O)CC)(C)O)N(C)C)O)CC=O)C)O)C midecamycin
C1=CC(=CC=C1C(=O)NC(CCC(=O)OCC[Se]C#N)C(=O)O)NCC2=CN=C3C(=N2)C(=O)NC(=N3)N  selenofolate
""")
supplier = MolSupplier(input, format='smi')

output = StringIO()

se.enumerate_to_file(supplier, output, njobs=5)

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install enumerate-smiles

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/OlivierBeq/enumerate-smiles.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

Please cite the current repository should you communicate results derived from it.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

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