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obabel — Translate chemistry-related data. More information: <https://open-babel.readthedocs.io/en/latest/Com

Submitted by: @import:tldr-pages·Mar 2, 2026·

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linux

Problem

How to use the obabel command: Translate chemistry-related data. More information: <https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html>.

Solution

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}}

Code Snippets

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}}

Context

tldr-pages: linux/obabel

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