learningmatter-mit
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chem-db-spectra
Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.
Vue d’ensemble
Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.
Lire la documentation complète
Documentation source, pas des instructions pour ce site. Vérifiez les permissions avant d’exécuter des commandes.
chem-db-spectra
Goal
To query experimental molecular spectra—such as Infrared (IR), Mass Spectrometry, and UV-Vis—from standard experimental databases like the NIST Chemistry WebBook for baseline comparison against properties computed via MLIPs or DFT.
Instructions
Step 1. Query Spectra Data
Use the query_spectra.py script to fetch available spectrographic data for a given chemical formula. The script automatically searches the NIST Chemistry WebBook, resolves the compound, and downloads all available JCAMP-DX (.jdx) formatted spectra into the specified directory.
# Env: base-agent
python .agents/skills/chem-db-spectra/scripts/query_spectra.py <formula> <output_dir> [--type {IR,Mass,UVVis,All}]
Parameters:
formula: The chemical formula to query (e.g.,CH4,C2H6O).output_dir: The directory path to save the downloaded JCAMP-DX (.jdx) spectrum files.--type: Filter the spectrum type to download (options:IR,Mass,UVVis,All). Default isAll.
Constraints
- Environments: The scripts require the
base-agentConda environment. - Spectrum Format: Output data is universally saved in JCAMP-DX (
.jdx) standard format. You must use appropriate spectroscopic python package (e.g.,jcamp) if you need to parse it back into numpy arrays. - Scraping Dependability: This script utilizes HTML scraping (
beautifulsoup4). If the NIST WebBook layout changes in the future, the selectors may need to be updated.
References
- Linstrom, P.J. and Mallard, W.G., Eds., NIST Chemistry WebBook, NIST Standard Reference Database Number 69, National Institute of Standards and Technology, Gaithersburg MD. URL
- JCAMP-DX for Infrared, Raman, and Related Data. URL
Author: Bowen Deng Contact: GitHub @learningmatter-mit
Métadonnées du fichier
name: chem-db-spectra description: Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules. category: chemistry
Voir le texte original
---
name: chem-db-spectra
description: Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.
category: chemistry
---
# chem-db-spectra
## Goal
To query experimental molecular spectra—such as Infrared (IR), Mass Spectrometry, and UV-Vis—from standard experimental databases like the NIST Chemistry WebBook for baseline comparison against properties computed via MLIPs or DFT.
## Instructions
### Step 1. Query Spectra Data
Use the `query_spectra.py` script to fetch available spectrographic data for a given chemical formula. The script automatically searches the NIST Chemistry WebBook, resolves the compound, and downloads all available JCAMP-DX (`.jdx`) formatted spectra into the specified directory.
```bash
# Env: base-agent
python .agents/skills/chem-db-spectra/scripts/query_spectra.py <formula> <output_dir> [--type {IR,Mass,UVVis,All}]
```
Parameters:
- `formula`: The chemical formula to query (e.g., `CH4`, `C2H6O`).
- `output_dir`: The directory path to save the downloaded JCAMP-DX (`.jdx`) spectrum files.
- `--type`: Filter the spectrum type to download (options: `IR`, `Mass`, `UVVis`, `All`). Default is `All`.
## Constraints
- **Environments**: The scripts require the `base-agent` Conda environment.
- **Spectrum Format**: Output data is universally saved in JCAMP-DX (`.jdx`) standard format. You must use appropriate spectroscopic python package (e.g., `jcamp`) if you need to parse it back into numpy arrays.
- **Scraping Dependability**: This script utilizes HTML scraping (`beautifulsoup4`). If the NIST WebBook layout changes in the future, the selectors may need to be updated.
## References
- Linstrom, P.J. and Mallard, W.G., Eds., *NIST Chemistry WebBook, NIST Standard Reference Database Number 69*, National Institute of Standards and Technology, Gaithersburg MD. [URL](https://webbook.nist.gov)
- JCAMP-DX for Infrared, Raman, and Related Data. [URL](https://jcamp-dx.org)
---
**Author:** Bowen Deng
**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)
Examiner la source
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- Licence
- MIT
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Réviser avant installation: Éviter l’installation automatique
Licence: MIT
- Dependency or permission surface needs review
- Permission surface may require sandboxing
- Financial research output is not financial advice; require human review before any live investment decision
- The script excerpt is truncated, but the full script is not provided for review; however, the described functionality appears safe.
- No explicit error handling or retry logic is mentioned for network failures or NIST unavailability.
- Financial research output is not financial advice; require human review before any live investment decision.
- 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
Les outils sont des indications de métadonnées, pas une compatibilité testée. Les prompts sont des suggestions.
Commencer par une petite tâche
- 1Lisez la source et confirmez entrées, résultats, dépendances et permissions.
- 2Demandez un plan à l’agent. Approuvez la configuration et les coûts avant un test isolé.
- 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
- Chemin des instructions
- .agents/skills/chem-db-spectra/SKILL.md @ d1f7ecfda2cd
Version déclarée dans le registre ; vérifiez les versions de la source.
Qualité
66/100
Prometteur
Confiance
55/100
Do not auto-install
Audit
71/100
Revue nécessaire
- Dependency or permission surface needs review
- Permission surface may require sandboxing
- Financial research output is not financial advice; require human review before any live investment decision
- The script excerpt is truncated, but the full script is not provided for review; however, the described functionality appears safe.
- No explicit error handling or retry logic is mentioned for network failures or NIST unavailability.
- Financial research output is not financial advice; require human review before any live investment decision.
- 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
- Verified installs
- —
- Résultats
- —
Copier ne signifie pas installer. Les compteurs nécessitent un rapport de réussite et ne garantissent pas la qualité globale.
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Plus de détails
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}Pour le créateur
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