learningmatter-mit

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chem-db-qmof

Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.

Revisar el código fuenteVer en GitHub
Precio sin confirmar★ 161 Estrellas de GitHubRegistro actualizado · 6 sept 2026agent-skill

Resumen

Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.

Leer documentación completa

Documentación de origen, no instrucciones para este sitio. Revisa los permisos antes de ejecutar comandos.

chem-db-qmof

Goal

To retrieve computational data and relaxed crystal structures (.cif) for roughly 20,000 Metal-Organic Frameworks (MOFs) that have been thoroughly characterized using DFT. QMOF is hosted by the Materials Project under the "MPContribs" project (qmof). This skill allows you to retrieve relaxed CIF structures by reference name, CSD refcode, or specific structural/electronic properties like bandgap.

Prerequisites

  • Dependency: mpcontribs-client must be installed.
  • Environment: Execution happens in the base-agent environment.
  • Credentials: Requires the standard Materials Project API key exported as MP_API_KEY.

Instructions

  1. Query Database: Use the provided script query_qmof.py to search by formula or identifier.
# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --formula "Zn" \
    --max-results 5 \
    --output-dir ./research/qmof_results
Available Arguments:
  • --formula: Search by chemical formula or elements (e.g., Zn,O,C).
  • --identifier: Search by specific CSD refcode or MOF common name (e.g., KAXQIL).
  • --max-results: Maximum number of structures to download (default: 5).
  • --output-dir: Directory to save the resulting .cif files.

Examples

Example 1: Automated testing script (Zinc MOF)

# Env: base-agent
bash .agents/skills/chem-db-qmof/examples/test_qmof.sh

Example 2: Query for 5 MOFs containing Zinc manually

# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --formula "Zn" \
    --max-results 5 \
    --output-dir ./results/qmof_zn

Example 2: Retrieve a specific MOF by identifier

# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --identifier "KAXQIL" \
    --max-results 1 \
    --output-dir ./results/qmof_kaxqil

Constraints

  • API Limits: The Materials Project/MPContribs API has rate limits. Do not use extremely large values for --max-results unless necessary.
  • Availability: If you cannot find a MOF in QMOF via the script, or if the API query is overly complex, you can also search the QMOF database manually through the Materials Project web interface under the "Contributions" section.

Author: Bowen Deng Contact: GitHub @learningmatter-mit

Metadatos del archivo
name: chem-db-qmof
description: Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.
category: [materials, chemistry]
Ver texto original
---
name: chem-db-qmof
description: Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.
category: [materials, chemistry]
---

# chem-db-qmof

## Goal

To retrieve computational data and relaxed crystal structures (.cif) for roughly 20,000 Metal-Organic Frameworks (MOFs) that have been thoroughly characterized using DFT. QMOF is hosted by the Materials Project under the "MPContribs" project (`qmof`). This skill allows you to retrieve relaxed CIF structures by reference name, CSD refcode, or specific structural/electronic properties like bandgap.

## Prerequisites

- **Dependency**: `mpcontribs-client` must be installed.
- **Environment**: Execution happens in the `base-agent` environment.
- **Credentials**: Requires the standard Materials Project API key exported as `MP_API_KEY`.

## Instructions

1. **Query Database**: Use the provided script `query_qmof.py` to search by formula or identifier.

```bash
# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --formula "Zn" \
    --max-results 5 \
    --output-dir ./research/qmof_results
```

### Available Arguments:
- `--formula`: Search by chemical formula or elements (e.g., `Zn,O,C`).
- `--identifier`: Search by specific CSD refcode or MOF common name (e.g., `KAXQIL`).
- `--max-results`: Maximum number of structures to download (default: 5).
- `--output-dir`: Directory to save the resulting `.cif` files.

## Examples

**Example 1: Automated testing script (Zinc MOF)**
```bash
# Env: base-agent
bash .agents/skills/chem-db-qmof/examples/test_qmof.sh
```

**Example 2: Query for 5 MOFs containing Zinc manually**
```bash
# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --formula "Zn" \
    --max-results 5 \
    --output-dir ./results/qmof_zn
```

**Example 2: Retrieve a specific MOF by identifier**
```bash
# Env: base-agent
python .agents/skills/chem-db-qmof/scripts/query_qmof.py \
    --identifier "KAXQIL" \
    --max-results 1 \
    --output-dir ./results/qmof_kaxqil
```

## Constraints

- **API Limits**: The Materials Project/MPContribs API has rate limits. Do not use extremely large values for `--max-results` unless necessary.
- **Availability**: If you cannot find a MOF in QMOF via the script, or if the API query is overly complex, you can also search the QMOF database manually through the Materials Project web interface under the "Contributions" section.

---

**Author:** Bowen Deng
**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)

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Licencia: MIT

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The SKILL.md example code block for 'Example 1' appears to have a formatting issue (unclosed code fence) in the provided excerpt, though the actual file may be correct.
  • The script snippet in the documentation is truncated, but the full script is present in the repository.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
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Empieza con una tarea pequeña

  1. 1Lee la fuente y confirma entradas, resultados, dependencias y permisos.
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  3. 3Comprueba resultados y archivos modificados. Informa solo de lo ejecutado y conserva la revisión de la fuente.

Consulta dependencias, claves API y costes externos en la fuente. Un repositorio público no implica servicios gratuitos.

Fuente y notas de uso

Indexado

Los metadatos y revisiones son orientativos. Popularidad, descubrimiento y ejecución correcta son hechos distintos.

Repositorio fuente
learningmatter-mit/AtomisticSkills
Licencia
MIT
Versión
1.0.0
Último push de GitHub
3 sept 2026
Registro actualizado
6 sept 2026

Versión declarada en el registro; consulta las versiones de la fuente.

Calidad

66/100

Prometedor

Confianza

56/100

Do not auto-install

Auditoría

72/100

Requiere revisión

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The SKILL.md example code block for 'Example 1' appears to have a formatting issue (unclosed code fence) in the provided excerpt, though the actual file may be correct.
  • The script snippet in the documentation is truncated, but the full script is present in the repository.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
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Más detalles
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Señal de comunidad

Comparte si este skill resulta útil para tu flujo de Agent. Los comentarios agregados mejoran la clasificación con el tiempo.