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.
Use this skill when the user provides a SMILES string and wants:
--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)/tmp/chemclaw/predicted_ms.msp/tmp/chemclaw/predicted_ms.mgf/tmp/chemclaw/predicted_ms.pngIf --output-stem mol1 is used, the outputs become:
/tmp/chemclaw/mol1.msp/tmp/chemclaw/mol1.mgf/tmp/chemclaw/mol1.pngWhen returning results to the user, include the generated spectrum image directly in the response when a PNG was created.
https://apps.bam.de/shn01/fioRa/.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
cd ms-spectra-simulation
python ms_spectra_simulation.py CCO
This uses:
name=mol1precursor=[M+H]+ce=20instrument=HCDcd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" \
--name mol1 \
--precursor "[M+H]+" \
--ce 20 \
--instrument HCD
cd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" --no-plot
cd ms-spectra-simulation
python ms_spectra_simulation.py "CCO" --show-title