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