Openbabel Agent Skill
> 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.
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill openbabelThe instruction itself
10 sections, as written by the authorOpen 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:
- Confirm source file(s) and desired target format.
- Prefer explicit
-iand-oformat flags for reproducibility. - Add
--gen3dwhen 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 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/
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How to use it
Take jinzhezenggroup/openbabel from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.
The instructions reference uvx.
Without those the skill loads but fails at the first command.