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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.

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Prix non confirmé★ 161 Stars GitHubRegistre mis à jour · 6 sept. 2026agent-skill

Vue d’ensemble

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.

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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

Métadonnées du fichier
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]
Voir le texte 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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Licence: 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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Commencer par une petite tâche

  1. 1Lisez la source et confirmez entrées, résultats, dépendances et permissions.
  2. 2Demandez un plan à l’agent. Approuvez la configuration et les coûts avant un test isolé.
  3. 3Vérifiez résultats et fichiers modifiés. Signalez uniquement ce qui a été exécuté et conservez la révision source.

Vérifiez les dépendances, clés API et frais externes dans la source. Un dépôt public ne rend pas tous les services gratuits.

Source et conseils d’utilisation

Répertorié

Métadonnées et examens sont indicatifs. Popularité, découverte et exécution réussie sont des faits distincts.

Dépôt source
learningmatter-mit/AtomisticSkills
Licence
MIT
Version
1.0.0
Dernier push GitHub
3 sept. 2026
Registre mis à jour
6 sept. 2026

Version déclarée dans le registre ; vérifiez les versions de la source.

Qualité

66/100

Prometteur

Confiance

56/100

Do not auto-install

Audit

72/100

Revue nécessaire

  • 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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Plus de détails
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