openbabel

name	openbabel
description	A versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D chemical structure images, and preparing or extracting structures for computational workflows. USE WHEN you need to convert between chemical file formats (e.g., xyz, pdb, mol, smi, gjf), generate 3D structures from SMILES using `--gen3d`, render molecule images (PNG/SVG), or extract geometries from simulation logs to build new inputs.
compatibility	Requires uv and internet access (uses `uvx --from openbabel obabel ...`).
license	LGPL-3.0-or-later
metadata	{"author":"njzjz-bot","version":"1.1","repository":"https://github.com/openbabel/openbabel"}

Open Babel

This skill provides practical Open Babel command patterns for common chemistry data tasks.

Quick Start

Check installation through uvx:

uvx --from openbabel obabel -V

Typical conversion syntax:

uvx --from openbabel obabel input.ext -i<input_format> -o<output_format> -O output.ext

Core Tasks

1) File format conversion

Convert XYZ to PDB:

uvx --from openbabel obabel C.xyz -ixyz -opdb -O C.pdb

Open Babel supports a large set of chemistry formats (e.g., xyz, mol, mol2, pdb, smi, Gaussian gjf/log/fchk, etc.).

2) Build structures from SMILES

Generate methane (3D coordinates required):

uvx --from openbabel obabel -:C --gen3d -omol -O C.mol

Generate a single carbon atom:

uvx --from openbabel obabel -:[C] --gen3d -omol -O C.mol

Generate methyl radical:

uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.mol

Important: quote SMILES when they contain brackets or special characters.

Equivalent explicit form:

uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.mol

3) Export SMILES from one or more structure files

uvx --from openbabel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smi

4) Render 2D structure images

Generate PNG:

uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -opng -O cys.png

Generate SVG:

uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -osvg -O cys.svg

Convert Gaussian log directly to image:

uvx --from openbabel obabel phosphate.log -ilog -opng -O phosphate.png

5) Gaussian workflow helper

Generate Gaussian input from SMILES, then patch header with sed:

uvx --from openbabel obabel -:CC --gen3d -ogjf | sed "1c %nproc=28\n#opt b3lyp/6-31g(d,p)" > CC.gjf

Generate next-step input from a previous Gaussian log:

uvx --from openbabel obabel CC.log -ilog -ogjf | sed "1c %nproc=28\n#freq b3lyp/6-31g(d,p)" > CC2.gjf

Agent Checklist

When using this skill for users:

1. Confirm source file(s) and desired target format.
2. Prefer explicit -i and -o format flags for reproducibility.
3. Add --gen3d when converting SMILES to coordinate-bearing structures.
4. Quote SMILES strings that contain brackets/parentheses.
5. For Gaussian workflows, verify route section and resource lines (%nproc, method/basis) after generation.
6. Use uvx --from openbabel obabel ... consistently to minimize local dependency setup.

References

• Open Babel project: https://openbabel.org/
• Open Babel GitHub: https://github.com/openbabel/openbabel
• openbabel package: https://pypi.org/project/openbabel/