ms-spectra-simulation

# 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) ```bash 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 ```bash 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 ```bash 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 ```bash cd ms-spectra-simulation python ms_spectra_simulation.py "CCO" --no-plot ``` ### Show the title on the figure ```bash cd ms-spectra-simulation python ms_spectra_simulation.py "CCO" --show-title ```