| 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=mol1precursor=[M+H]+ce=20instrument=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
