SMILES to Atoms

Conversion of SMILES to ASE’s Atoms is done via RDKit. To install:

conda install -c conda-forge rdkit

Command line

wfl generate-configs smiles -o configs.xyz CCCCCC CC c1ccccc1

Python script

Single operation:

from wfl.generate import smiles
atoms = smiles.smi_to_atoms("CCCCCC")

With Workflow’s parallelization:

from wfl.configset import ConfigSet
from wfl.generate import smiles

outputspec = OutputSpec("compounds.xyz")
smiles = ["CO", "CCCC", "c1ccccc1"]
smiles.smiles(smiles, outputs=outputspec)

NB smiles has to be given as the first argument.