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SKILL verified MIT Self-run

Ms Spectra Simulation

skill-internscience-chemclaw-ms-spectra-simulation · by InternScience

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.

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Install

$ agentstack add skill-internscience-chemclaw-ms-spectra-simulation

✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

View the full security report →

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Reliability & compatibility

✓ Security review passed
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Declared compatibility

Claude CodeClaude Desktop

Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.

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About

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

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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