obabel

Translate chemistry-related data. More information: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html.

• Convert a .mol file to XYZ coordinates:

obabel path/to/file.mol -O path/to/output_file.xyz

• Convert a SMILES string to a 500x500 picture:

obabel -:"SMILES" -O path/to/output_file.png -xp 500

• Convert a file of SMILES string to separate 3D .mol files:

obabel path/to/file.smi -O path/to/output_file.mol --gen3D -m

• Render multiple inputs into one picture:

obabel path/to/file1 path/to/file2 … -O path/to/output_file.png