obabel

Translate chemistry-related data. More information: https://openbabel.org/wiki/Main_Page.

• 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}}