chem-db-spectra

Download molecular IR, Mass, and UV-Vis spectra as JCAMP-DX files from the NIST Chemistry WebBook.

144|21|Updated Jan 8, 2026
One-click install
npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill chem-db-spectra
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: chem-db-spectra
Source: https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-db-spectra
Command: npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill chem-db-spectra

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, beautifulsoup4, argparse, json, os, and includes scripts (resource) components.

What problem does it solve?

Chemists and materials researchers often need experimental IR, Mass, and UV-Vis spectra quickly to benchmark computed or simulated molecular properties, but manually searching and downloading spectra is slow and error-prone.

Core Features & Use Cases

  • Experimental spectral lookup: Finds matching compounds in the NIST Chemistry WebBook by chemical formula and downloads available spectra.
  • JCAMP-DX acquisition: Retrieves spectra in JCAMP-DX (.jdx) format for IR, Mass spectrometry, and UV-Vis so you can compare against MLIP/DFT predictions.
  • Reproducible downloads: Saves the input parameters alongside downloaded outputs for traceability.
  • Use Case: For a given molecule formula (e.g., C2H6O), automatically collect all available IR, Mass, and UV-Vis reference spectra to validate computed vibrational features or electronic transitions.

Quick Start

Use the base-agent environment to run python .agents/skills/chem-db-spectra/scripts/query_spectra.py CH4 output_spectra/ --type All to download all available JCAMP-DX spectra for methane into output_spectra/.

Frequently Asked Questions about chem-db-spectra

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I download experimental molecular spectra from the NIST WebBook?

You can download experimental molecular spectra from the NIST WebBook by running the query_spectra.py script with a chemical formula and output directory. It queries NIST and saves the spectra locally.

Can I retrieve JCAMP-DX files for IR, Mass, and UV-Vis spectra automatically?

Yes, you can retrieve JCAMP-DX files automatically by executing the script with the --type flag set to IR, Mass, UVVis, or All. It downloads available reference spectra in .jdx format.

How do I get reference spectra for benchmarking AI-driven molecular property predictions?

To get reference spectra for benchmarking, provide a chemical formula to the query script. It fetches experimental IR, Mass, and UV-Vis data from NIST, saving reproducible inputs and outputs for validation.

Do I need a specific environment to run the NIST spectra query script?

Yes, you need a base-agent environment to execute the Python script. The tool relies on the requests and beautifulsoup4 libraries to query the NIST Chemistry WebBook and download spectra files.

What types of experimental spectra can I filter for when querying chemical formulas?

You can filter experimental spectra by type using the --type argument. Available options include IR, Mass, UVVis, and All, allowing targeted retrieval of specific reference data from the NIST Chemistry WebBook.

Are downloaded NIST spectra inputs saved for traceability?

Yes, downloaded NIST spectra inputs are saved for traceability. The tool saves the input parameters alongside the downloaded JCAMP-DX outputs to ensure reproducible benchmarking workflows.