openbabel - SKILL.md Agent Skill

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-wheel obabel ...`). license: LGPL-3.0-or-later metadata: author: njzjz-bot version: '1.1' repository: https://github.com/openbabel/openbabel

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

Check installation through uvx:

uvx --from openbabel-wheel obabel -V

Typical conversion syntax:

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

Convert XYZ to PDB:

uvx --from openbabel-wheel 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.).

Generate methane (3D coordinates required):

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

Generate a single carbon atom:

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

Generate methyl radical:

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

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

Equivalent explicit form:

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

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

Generate PNG:

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

Generate SVG:

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

Convert Gaussian log directly to image:

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

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

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

When using this skill for users:

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