--- 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 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 obabel -V ```

Typical conversion syntax:

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

Generate a single carbon atom:

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

Generate methyl radical:

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

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

Equivalent explicit form:

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

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

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

### 4) Render 2D structure images

Generate PNG:

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

Generate SVG:

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

Convert Gaussian log directly to image:

```bash uvx --from openbabel 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 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 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 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/

--- 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 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 obabel -V ```

Typical conversion syntax:

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

Generate a single carbon atom:

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

Generate methyl radical:

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

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

Equivalent explicit form:

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

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

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

### 4) Render 2D structure images

Generate PNG:

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

Generate SVG:

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

Convert Gaussian log directly to image:

```bash uvx --from openbabel 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 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 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 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/

--- 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 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 obabel -V ```

Typical conversion syntax:

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

Generate a single carbon atom:

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

Generate methyl radical:

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

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

Equivalent explicit form:

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

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

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

### 4) Render 2D structure images

Generate PNG:

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

Generate SVG:

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

Convert Gaussian log directly to image:

```bash uvx --from openbabel 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 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 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 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/

--- 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 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 obabel -V ```

Typical conversion syntax:

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

Generate a single carbon atom:

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

Generate methyl radical:

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

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

Equivalent explicit form:

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

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

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

### 4) Render 2D structure images

Generate PNG:

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

Generate SVG:

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

Convert Gaussian log directly to image:

```bash uvx --from openbabel 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 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 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 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/