Sync from GitHub: Update project structure in README for mixin modules

.last_sync

@@ -1 +1 @@
-1ba9fe091732330384694b2f4d259c9efde1f1ae
+7670616ff77a08e7bdcd07b34899636485b19e20

README.md

@@ -20,14 +20,22 @@ A web-based application for analyzing nucleic acid (DNA/XNA)-silver complexes an
 
 ```
 NucleoSpec/
-├── dna_silver_webapp.py    # Main Flask application
+├── dna_silver_webapp.py       # Main Flask application
 ├── core/
-│   └── analyzer.py         # DNASilverAnalyzer class (analysis logic)
+│   ├── analyzer.py            # DNASilverAnalyzer class (composition search)
+│   ├── spectrum.py            # SpectrumMixin: parsing, peak detection
+│   ├── envelope.py            # EnvelopeMixin: Gaussian fitting, symmetry
+│   ├── scoring.py             # ScoringMixin: pattern similarity, scoring
+│   ├── isotope.py             # IsotopeMixin: isotope pattern generation
+│   ├── charge.py              # ChargeMixin: charge state detection
+│   ├── adducts.py             # AdductMixin: custom adduct CRUD
+│   └── dna.py                 # DNAMixin: DNA/XNA composition helpers
 ├── lib/
-│   └── pythoms/            # PythoMS library (isotope calculations)
-├── templates/              # HTML templates
-├── sample_data/            # Example spectrum files
-└── environment_hf.yml      # HuggingFace deployment environment
+│   └── pythoms/               # PythoMS library (isotope calculations)
+├── templates/
+│   └── index.html             # Single-page frontend (Plotly.js, JSME)
+├── sample_data/               # Example spectrum files
+└── environment_hf.yml         # HuggingFace deployment environment
 ```
 
 ## Installation
@@ -108,6 +116,12 @@ Supported formats: .txt, .csv
 - **Frontend:** HTML5, JavaScript, Plotly.js, JSME
 - **Libraries:** PythoMS, IsoSpecPy
 
+## Citation
+
+If you use NucleoSpec in a publication, please cite:
+
+> Lin, I.-H.; Copp, S. M. A Tutorial on Automated Mass Spectral Analysis using NucleoSpec for Compositional Assignment of Nucleic Acid–Silver Complexes and Nanoclusters. *ChemRxiv* 2026. [DOI: 10.26434/chemrxiv.15004738/v1](https://doi.org/10.26434/chemrxiv.15004738/v1)
+
 ## Support
 
 - **Developer:** I-Hsin (Vivian) Lin