Molecode
AtomFlow-AI/MoleCode
A skill your agent uses for deterministic molecule understanding, graph-level editing, generation, and validation with MoleCode — an explicit Mermaid graph in which every atom and bond is a typed…
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…
Install Openbabel
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills openbabel --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/data-processing/openbabel .claude/skills/openbabel && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "openbabel" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/openbabel into .claude/skills/openbabel/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "openbabel", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/openbabelType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills openbabel --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/data-processing/openbabel .agents/skills/openbabel && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "openbabel" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/openbabel into .agents/skills/openbabel/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "openbabel", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills openbabel --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/data-processing/openbabel .cursor/skills/openbabel && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "openbabel" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/openbabel into .cursor/skills/openbabel/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "openbabel", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git --path data-processing/openbabel--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills openbabel --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/data-processing/openbabel .gemini/skills/openbabel && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "openbabel" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/openbabel into .gemini/skills/openbabel/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "openbabel", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills openbabelInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/data-processing/openbabel .github/skills/openbabel && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "openbabel" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/openbabel into .github/skills/openbabel/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "openbabel", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills openbabel --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/data-processing/openbabel .opencode/skills/openbabel && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "openbabel" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/openbabel into .opencode/skills/openbabel/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "openbabel", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
openbabel- GitHub stars
- 148
- Token cost
- ~850 tokens
- SKILL.md length
- 209 words
- Files
- 1
- Skills in repo
- 62
- Repo updated
- First seen
- Licence
- LGPL-3.0-or-later
At a glance
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…
- Works in 5 steps: File format conversion → Build structures from SMILES → Export SMILES from one or more structure… → …
- You need to convert between chemical file formats (e.g.
- SKILL.md covers Quick Start, Core Tasks, Agent Checklist and References
- Calls uvx
What it does
Openbabel is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. 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.
Its SKILL.md is about 850 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts. Compatibility notes: Requires uv and internet access (uses uvx --from openbabel obabel ...).
It sits in Research & Science, covering Drug discovery and cheminformatics. The repository describes itself as: Agent skills to run computational-chemistry tasks, used in OpenClaw. The licence is LGPL-3.0-or-later.
When your agent uses it
- You need to convert between chemical file formats (e.g.
- Generate 3D structures from SMILES using --gen3d
- Render molecule images (PNG/SVG)
- Extract geometries from simulation logs to build new inputs
Example prompts
- “/openbabel”
Requirements
- Compatibility (from SKILL.md): Requires uv and internet access (uses `uvx --from openbabel obabel ...`).
Workflow steps
5 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 5c19e75. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
uvx
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
openbabel.orggithub.compypi.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Compatibility
Requires uv and internet access (uses `uvx --from openbabel obabel ...`).
From compatibility in the SKILL.md frontmatter.
Context cost
Openbabel loads about 850 tokens when it runs. Until then it costs about 116 tokens; SKILL.md has 209 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from jinzhezenggroup/computational-chemistry-agent-skills at commit 5c19e75, republished under its LGPL-3.0-or-later licence (© jinzhezenggroup). 209 words, ~850 tokens.
Download SKILL.mdSave it as
.claude/skills/openbabel/SKILL.md (or your agent's skills folder).- 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
- metadata.version
- 1.1
- metadata.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 -VTypical conversion syntax:
uvx --from openbabel obabel input.ext -i<input_format> -o<output_format> -O output.extCore Tasks
1) File format conversion
Convert XYZ to PDB:
uvx --from openbabel obabel C.xyz -ixyz -opdb -O C.pdbOpen 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.molGenerate a single carbon atom:
uvx --from openbabel obabel -:[C] --gen3d -omol -O C.molGenerate methyl radical:
uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.molImportant: quote SMILES when they contain brackets or special characters.
Equivalent explicit form:
uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.mol3) Export SMILES from one or more structure files
uvx --from openbabel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smi4) Render 2D structure images
Generate PNG:
uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -opng -O cys.pngGenerate SVG:
uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -osvg -O cys.svgConvert Gaussian log directly to image:
uvx --from openbabel obabel phosphate.log -ilog -opng -O phosphate.png5) 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.gjfGenerate 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.gjfAgent 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/
© jinzhezenggroup, LGPL-3.0-or-later. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in data-processing/openbabel of jinzhezenggroup/computational-chemistry-agent-skills.
Open the folder on GitHubat commit 5c19e75
Compare with similar skills
Openbabel next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Openbabel this skilljinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~850 | Automated safety check: Pass | LGPL-3.0-or-later | |
| MolecodeAtomFlow-AI/MoleCode | 306 | — | ~1.9k | Automated safety check: Pass | MIT | |
| Drug DiscoveryTommy-yw/RunbookHermes | 546 | 1 repos | ~2.3k | Automated safety check: Pass | MIT | |
| DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3k | Automated safety check: Notes | MIT | |
| Biomedical Analysis Dispatchxjtulyc/MedgeClaw | 617 | 1 repos | ~2k | Automated safety check: Pass | None | |
| Biopipelineslocbp-uzh/biopipelines | 109 | — | ~2.4k | Automated safety check: Pass | MIT |
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Drug Discovery
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DiffDock Molecular Docking
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Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.
Biomedical Analysis Dispatch
xjtulyc/MedgeClaw
Routes bioinformatics, drug discovery, clinical and multi-omics tasks from a chat interface to Claude Code sessions running K-Dense scientific skills, with a live dashboard per task.
Biopipelines
locbp-uzh/biopipelines
Design and run computational protein and ligand workflows on a GPU: binder and enzyme design, de novo backbone generation, inverse folding and sequence redesign, structure prediction, protein-ligand…
Tooluniverse Chemical Compound Retrieval
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Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment.
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Turns a user-supplied atomic structure and DFT settings into a runnable Quantum ESPRESSO input file, stopping short of submitting the job.
DP-GEN Simplify Workflow
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Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs.
LAMMPS with DeePMD-kit
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Prepares and runs molecular dynamics simulations in LAMMPS with a DeePMD machine-learning potential, writing the input script and choosing NVE, NVT or NPT.
LAMMPS ReaxFF Setup
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Prepares and explains LAMMPS input scripts for reactive molecular dynamics with the ReaxFF potential, including charge equilibration and ensemble choice.
RDKit Conformer Generator
jinzhezenggroup/computational-chemistry-agent-skills
Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails.
RDKit Descriptors and Fingerprints
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Computes RDKit physicochemical descriptors and molecular fingerprints from SMILES through a uv-run CLI script that skips and logs invalid molecules.
Related
Categories
Questions about Openbabel
What does Openbabel do?
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…. Openbabel is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. 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.
When should I use Openbabel?
Openbabel fits situations like: you need to convert between chemical file formats (e.g; generate 3D structures from SMILES using --gen3d; render molecule images (PNG/SVG); extract geometries from simulation logs to build new inputs.
How do I install Openbabel in Claude Code?
Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a claude-code`. Or copy the skill folder (data-processing/openbabel in jinzhezenggroup/computational-chemistry-agent-skills) into .claude/skills/openbabel in your project. Claude Code loads it when a task matches its description.
How do I install Openbabel in Codex?
Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a codex`. Or copy the skill folder (data-processing/openbabel in jinzhezenggroup/computational-chemistry-agent-skills) into .agents/skills/openbabel in your project. Codex loads it when a task matches its description.
Can I use Openbabel in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/openbabel, .gemini/skills/openbabel, .github/skills/openbabel and .opencode/skills/openbabel in your project.
What does Openbabel need to run?
Going by SKILL.md and its folder, Openbabel needs the command-line tools its instructions call (uvx). Compatibility (from SKILL.md): Requires uv and internet access (uses `uvx --from openbabel obabel ...`)..
Does Openbabel access the network?
SKILL.md names 3 domains. As links in the text: openbabel.org, github.com and pypi.org. This is read from the text; nothing was executed.
Is Openbabel safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Openbabel use?
Openbabel is published under the LGPL-3.0-or-later licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Openbabel use?
About 850 tokens (SKILL.md is roughly 3.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Openbabel?
Skills that share tags, products or a category with Openbabel: Molecode (AtomFlow-AI/MoleCode, 306 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars), DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Openbabel?
jinzhezenggroup (a GitHub organization) maintains it in jinzhezenggroup/computational-chemistry-agent-skills, which has 148 GitHub stars. The repository holds 62 skills in this directory. The repository was last updated on October 9, 2026.
Source: jinzhezenggroup/computational-chemistry-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.