I wrote a little script to print out the SMILES string from an sdf file. For more information, see this blog post.

The script can read in a single SDF file that contains one or more molecules. There are two main ways to use this script. You can either call it directly with Python or use docker.

First, create an environment with the necessary dependencies and activate it:

$ micromamba create -n sdf2smiles --file environment.yaml
$ micromamba activate sdf2smiles

Then run the script:

$ python convert.py ethane.sdf
Converting ethane_template.sdf to SMILES
ethane: [H][C]([H])([H])[C]([H])([H])[H]

You can use this script without installing anything by using docker:

$ docker run --rm -v$(pwd):/opt/app mmh42/sdf2smiles:latest ethane.sdf
Converting ethane_template.sdf to SMILES
ethane: [H][C]([H])([H])[C]([H])([H])[H]

This example assumes you have a ethane.sdf in your current directory. You can change $(pwd) to point to a different local directory to read SDF files from.