ms-spectra-simulation

name	ms-spectra-simulation
description	Predict and visualize MS/MS spectra from a single SMILES using the fioRa online app. Use when the user wants a mass spectrum, MGF/MSP output, or a plotted stick spectrum from SMILES, with optional custom Name, precursor type, collision energy, and instrument settings.

MS Spectra Simulation Skill

When to use this

Use this skill when the user provides a SMILES string and wants:

• Predicted MS/MS spectrum
• Raw MSP output downloaded from fioRa
• Standard MGF output
• A quick stick-spectrum PNG visualization
• Simple defaults without manually preparing a CSV

Inputs

• SMILES string (required)
• --name (optional, default: mol1)
• --precursor (optional, default: [M+H]+)
• --ce (optional, default: 20)
• --instrument (optional, default: HCD)
• --output-stem (optional, default: predicted_ms)
• --plot / --no-plot (optional, default: plot enabled)
• --show-title / --no-show-title (optional, default: no title on the plot)

Outputs

• /tmp/chemclaw/predicted_ms.msp
• /tmp/chemclaw/predicted_ms.mgf
• /tmp/chemclaw/predicted_ms.png

If --output-stem mol1 is used, the outputs become:

• /tmp/chemclaw/mol1.msp
• /tmp/chemclaw/mol1.mgf
• /tmp/chemclaw/mol1.png

Agent response

When returning results to the user, include the generated spectrum image directly in the response when a PNG was created.

Notes

• This skill calls the fioRa online app at https://apps.bam.de/shn01/fioRa/.
• The site is a Shiny web app, so this skill uses Playwright browser automation instead of a simple REST request.
• Network access is required.

New environment (from zero)

conda create -n fiora-online python=3.10 pip -y
conda activate fiora-online

cd ms-spectra-simulation
python -m pip install -r requirements.txt
python -m playwright install chromium
python ms_spectra_simulation.py CCO

• Run the script in an environment with browser access.

How to use (environment already prepared)

Fastest default run

cd ms-spectra-simulation
python ms_spectra_simulation.py CCO

This uses:

• name=mol1
• precursor=[M+H]+
• ce=20
• instrument=HCD
• plot enabled
• plot title hidden
• fioRa online backend

Custom metadata

cd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" \
  --name mol1 \
  --precursor "[M+H]+" \
  --ce 20 \
  --instrument HCD

Keep the spectrum but skip PNG

cd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" --no-plot

Show the title on the figure

cd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" --show-title