openbabel ยท diff
v1.1 to v1.1
3 added, 1 removed. Audit A to A.
---
name: openbabel
- description: Use Open Babel CLI to convert molecular file formats, generate 3D structures from SMILES, render 2D structure images, and prepare Gaussian input files for computational chemistry workflows.
+ 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 ...`).
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/