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 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
- JCAMP-DX for Infrared, Raman, and Related Data. URL
Author: Bowen Deng
Contact: GitHub @learningmatter-mit
1---2name: chem-db-spectra3description: Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.4---56# chem-db-spectra78## Goal9To 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.1011## Instructions1213### Step 1. Query Spectra Data1415Use 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.1617```bash18# Env: base-agent19python .agents/skills/chem-db-spectra/scripts/query_spectra.py <formula> <output_dir> [--type {IR,Mass,UVVis,All}]20```2122Parameters:23- `formula`: The chemical formula to query (e.g., `CH4`, `C2H6O`).24- `output_dir`: The directory path to save the downloaded JCAMP-DX (`.jdx`) spectrum files.25- `--type`: Filter the spectrum type to download (options: `IR`, `Mass`, `UVVis`, `All`). Default is `All`.2627## Constraints28- **Environments**: The scripts require the `base-agent` Conda environment.29- **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.30- **Scraping Dependability**: This script utilizes HTML scraping (`beautifulsoup4`). If the NIST WebBook layout changes in the future, the selectors may need to be updated.3132## References33- 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)34- JCAMP-DX for Infrared, Raman, and Related Data. [URL](https://jcamp-dx.org)3536---3738**Author:** Bowen Deng39**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)
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