Add agentic-created pyopenms scripts for proteomics and metabolomics

[Copilot]

Bootstraps the repository with a practical collection of pyopenms-based scripts covering the core analytical tasks proteomics and metabolomics users need day-to-day. Each script lives in its own subdirectory following the per-script directory structure established in main.

Proteomics (scripts/proteomics/)

• peptide_mass_calculator/ – monoisotopic/average masses and b/y fragment ion series; supports modified sequences (e.g. PEPTM[147]IDEK) and arbitrary charge states
• protein_digest/ – in-silico enzymatic digestion against pyopenms ProteaseDB (30+ enzymes); configurable missed cleavages and length filters
• spectrum_file_info/ – mzML summary: MS-level counts, RT/m/z ranges, TIC statistics
• feature_detection_proteomics/ – FeatureFinderCentroided wrapper; outputs featureXML

Metabolomics (scripts/metabolomics/)

• metabolite_feature_detection/ – full FeatureFinderMetabo pipeline (mass tracing → elution peak detection → feature finding)
• mass_accuracy_calculator/ – ppm error between theoretical m/z (from sequence or molecular formula) and one or more observed values
• isotope_pattern_matcher/ – theoretical isotope distributions via CoarseIsotopePatternGenerator; cosine similarity scoring against observed peaks

Example

# Peptide masses + fragment ions
python scripts/proteomics/peptide_mass_calculator/peptide_mass_calculator.py --sequence PEPTIDEK --charge 2 --fragments

# ppm error for glucose
python scripts/metabolomics/mass_accuracy_calculator/mass_accuracy_calculator.py --formula C6H12O6 --observed 181.0709 181.0715

# Isotope pattern with similarity score
python scripts/metabolomics/isotope_pattern_matcher/isotope_pattern_matcher.py --formula C12H22O11 \
    --peaks 341.1056,100.0 342.1089,13.1

Also included

• Per-script requirements.txt and isolated test suites following the repository convention
• Per-script and top-level READMEs
• GitHub Actions CI workflow integration (via main merge)

Original prompt

A repository of agentic-created scripts using pyopenms interesting for proteomics and metabolomics users.

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[ypriverol]

@copilot Can you update your branch from main.

[Copilot]

@copilot Can you update your branch from main.

Done — merged origin/main into this branch in commit 4b04a21. Resolved the single README conflict by taking main's version, and removed the old flat script/test layout in favour of the per-script directory structure that landed on main.

[ypriverol]

@copilot Can you make sure you follow the standards of the main repository? Also make sure your script is not similar to any script in the repo.