Openbabel

What it does

When your agent uses it

• Tasks that involve Drug discovery and cheminformatics

Example prompts

• “/openbabel”

Requirements

• Python 3
• Compatibility (from SKILL.md): Requires Open Babel installed (apt install openbabel or conda install openbabel). Python bindings optional (pip install openbabel-wheel).

Workflow steps

2 steps, taken from the first numbered list in SKILL.md.

1. 1Open Babel installed (obabel -V)
2. 2For Python scripting: openbabel or openbabel-wheel package

What it can do on your machine

Read from SKILL.md and the folder at commit fd6291b. 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

  No scripts in the folder and no shell commands in SKILL.md (its code samples are bash and python).

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  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 Open Babel installed (apt install openbabel or conda install openbabel). Python bindings optional (pip install openbabel-wheel).

  From compatibility in the SKILL.md frontmatter.

Context cost

Openbabel loads about 1k tokens when it runs. Until then it costs about 47 tokens; SKILL.md has 304 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~47

When it runs · the whole SKILL.md, loaded when a task matches

~1k

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

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 Hello-QM/catgo-LRG at commit fd6291b, republished under its AGPL-3.0 licence (© Hello-QM). 304 words, ~1,002 tokens.

name

openbabel

description

Convert molecular file formats using Open Babel. Handles SMILES, mol2, sdf, pdb, xyz, cif, and 100+ other formats. Also performs 3D coordinate generation and hydrogen addition.

compatibility

Requires Open Babel installed (apt install openbabel or conda install openbabel). Python bindings optional (pip install openbabel-wheel).

catalog-hidden

true

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "convert_format",
  "command": "obabel input.mol2 -O output.pdb",
  "system_name": "format_convert"
})

obabel -:"CCO" -O ethanol.xyz --gen3d
# Generates 3D coordinates using force field optimization

obabel input.pdb -O output.pdb -h
# -h adds hydrogens at pH 7.4

obabel input.pdb -O output.pdb -d

obabel *.mol2 -O output_.pdb -m
# -m produces one output file per input molecule

obabel input.sdf -O conformers.sdf --conformer --nconf 50 --writeconformers

obabel input.mol2 -O output.smi -ocan

obabel input.xyz -O minimized.xyz --minimize --ff MMFF94 --steps 2500

from openbabel import openbabel as ob

conv = ob.OBConversion()
conv.SetInFormat("smi")
conv.SetOutFormat("mol2")

mol = ob.OBMol()
conv.ReadString(mol, "c1ccccc1")  # benzene

# Generate 3D
builder = ob.OBBuilder()
builder.Build(mol)

# Force field optimization
ff = ob.OBForceField.FindForceField("MMFF94")
ff.Setup(mol)
ff.ConjugateGradients(500)
ff.GetCoordinates(mol)

conv.WriteFile(mol, "benzene.mol2")

© Hello-QM, AGPL-3.0. 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 .claude/skills/openbabel of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b

Used in 1 other repository

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in Hello-QM/catgo-LRG, which our catalogue first saw on October 7, 2026.

• majiayu000/claude-skill-registryskills/bash/openbabel