# Gjf To Xyz

> |

- **Type:** Skill
- **Install:** `agentstack add skill-internscience-chemclaw-gjf-to-xyz`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [InternScience](https://agentstack.voostack.com/s/internscience)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [InternScience](https://github.com/InternScience)
- **Source:** https://github.com/InternScience/ChemClaw/tree/main/skills/gjf-to-xyz

## Install

```sh
agentstack add skill-internscience-chemclaw-gjf-to-xyz
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# GJF to XYZ Converter

Convert Gaussian gjf files to XYZ format. Supports single file conversion and batch processing.

## Quick Start

### Command Line

```bash
# Single file conversion
python scripts/gjf2xyz.py input.gjf

# Specify output file
python scripts/gjf2xyz.py input.gjf -o output.xyz

# Batch conversion
python scripts/gjf2xyz.py ./gjf_directory/ -o ./xyz_directory/
```

### Python API

```python
from scripts.gjf2xyz import convert_gjf_to_xyz, batch_convert

# Convert single file
output_path = convert_gjf_to_xyz("molecule.gjf", "molecule.xyz")

# Batch conversion
converted_files = batch_convert("./gjf_files/", "./xyz_files/")
```

## File Formats

### Input: GJF (Gaussian Input)
```
%chk=molecule.chk
# hf/3-21g

Title Card Required

0 1
 C     2.21210000    0.98250000   -0.58720000
 H     2.46010000    0.50290000    0.38600000
...
```

### Output: XYZ
```
56
Title Card Required
 C      2.21210000    0.98250000   -0.58720000
 H      2.46010000    0.50290000    0.38600000
...
```

## Features

- Extracts atomic coordinates from Gaussian gjf files
- Preserves element symbols and coordinates
- Extracts title from gjf file
- Handles connectivity section (ignored in output)
- Batch processing support
- Automatic output naming

## Notes

- XYZ format contains only element symbol and coordinates
- Charge and multiplicity information is not preserved in XYZ
- Connectivity information is ignored during conversion

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [InternScience](https://github.com/InternScience)
- **Source:** [InternScience/ChemClaw](https://github.com/InternScience/ChemClaw)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-internscience-chemclaw-gjf-to-xyz
- Seller: https://agentstack.voostack.com/s/internscience
- Browse the marketplace: https://agentstack.voostack.com/browse

---
Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.