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openbabel
80 / 100 · Low risk
Fine to try.
By jinzhezenggroup/computational-chemistry-agent-skills (GitHub) · media · 157 stars · scanned at commit 8ab83a9
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.
Works with any agent that supports SKILL.md skills.
What this skill can do
Downloads and installs other software
The author does not mention this.
Found in 15 places.
Show 12 more
- data-processing/openbabel/SKILL.md, line 39
uvx --from openbabel obabel C.xyz -ixyz -opdb -O C.pdb - data-processing/openbabel/SKILL.md, line 49
uvx --from openbabel obabel -:C --gen3d -omol -O C.mol - data-processing/openbabel/SKILL.md, line 55
uvx --from openbabel obabel -:[C] --gen3d -omol -O C.mol - data-processing/openbabel/SKILL.md, line 61
uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.mol - data-processing/openbabel/SKILL.md, line 69
uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.mol - data-processing/openbabel/SKILL.md, line 75
uvx --from openbabel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smi - data-processing/openbabel/SKILL.md, line 83
uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -opng -O cys.png - data-processing/openbabel/SKILL.md, line 89
uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -osvg -O cys.svg - data-processing/openbabel/SKILL.md, line 95
uvx --from openbabel obabel phosphate.log -ilog -opng -O phosphate.png - data-processing/openbabel/SKILL.md, line 103
uvx --from openbabel obabel -:CC --gen3d -ogjf | sed "1c %nproc=28\n#opt b3lyp/6-31g(d,p)" > CC.gjf - data-processing/openbabel/SKILL.md, line 109
uvx --from openbabel obabel CC.log -ilog -ogjf | sed "1c %nproc=28\n#freq b3lyp/6-31g(d,p)" > CC2.gjf - data-processing/openbabel/SKILL.md, line 121
1. Use `uvx --from openbabel obabel ...` consistently to minimize local dependency setup.
Runs commands on your computer
The author does not mention this.
Found in 13 places.
Show 10 more
- data-processing/openbabel/SKILL.md, line 49
uvx --from openbabel obabel -:C --gen3d -omol -O C.mol - data-processing/openbabel/SKILL.md, line 55
uvx --from openbabel obabel -:[C] --gen3d -omol -O C.mol - data-processing/openbabel/SKILL.md, line 61
uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.mol - data-processing/openbabel/SKILL.md, line 69
uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.mol - data-processing/openbabel/SKILL.md, line 75
uvx --from openbabel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smi - data-processing/openbabel/SKILL.md, line 83
uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -opng -O cys.png - data-processing/openbabel/SKILL.md, line 89
uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -osvg -O cys.svg - data-processing/openbabel/SKILL.md, line 95
uvx --from openbabel obabel phosphate.log -ilog -opng -O phosphate.png - data-processing/openbabel/SKILL.md, line 103
uvx --from openbabel obabel -:CC --gen3d -ogjf | sed "1c %nproc=28\n#opt b3lyp/6-31g(d,p)" > CC.gjf - data-processing/openbabel/SKILL.md, line 109
uvx --from openbabel obabel CC.log -ilog -ogjf | sed "1c %nproc=28\n#freq b3lyp/6-31g(d,p)" > CC2.gjf
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'openbabel' ] || [ -L ~/.agents/skills/'openbabel' ]; then echo 'A skill folder named openbabel already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/jinzhezenggroup/computational-chemistry-agent-skills' "$d" && git -C "$d" checkout --quiet '8ab83a96292bb4d13ba7e4a2b015015f0332e8cc' -- 'data-processing/openbabel' && mkdir -p ~/.agents/skills && cp -R "$d"/'data-processing/openbabel' ~/.agents/skills/'openbabel' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'openbabel' ~/.claude/skills/'openbabel' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for jinzhezenggroup/computational-chemistry-agent-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/jinzhezenggroup/computational-chemistry-agent-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 8ab83a9 | 80 |