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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}}