openbabel v1.1A

Immutable. This exact content is served forever at /api/v1/blob/7fbb3438f4d136ce.

---
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
---

# Open Babel

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

## Quick Start

Check installation through uvx:

```bash
uvx --from openbabel-wheel obabel -V
```

Typical conversion syntax:

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

## Core Tasks

### 1) File format conversion

Convert XYZ to PDB:

```bash
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.).

### 2) Build structures from SMILES

Generate methane (3D coordinates required):

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

Generate a single carbon atom:

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

Generate methyl radical:

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

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

Equivalent explicit form:

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

### 3) Export SMILES from one or more structure files

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

### 4) Render 2D structure images

Generate PNG:

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

Generate SVG:

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

Convert Gaussian log directly to image:

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

### 5) Gaussian workflow helper

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

```bash
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:

```bash
uvx --from openbabel-wheel 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:

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

## References

- Open Babel project: https://openbabel.org/
- Open Babel GitHub: https://github.com/openbabel/openbabel
- openbabel-wheel package: https://pypi.org/project/openbabel-wheel/