stacking_model.py

#!/usr/bin/env python3
"""
stacking_model.py — RNA dinucleotide stacking free-energy model for DGD
========================================================================
Author : Vipin Menon, BIG Lab, Hanyang University
Date   : August 2021 (modernized 2026)

Provides `return_stacking_model()` which returns a dictionary-of-dictionaries
mapping RNA dinucleotide pairs to their stacking free energies (kcal/mol).
"""


def return_stacking_model() -> dict:
    """
    Return the RNA stacking free-energy model.

    Constructs and returns a nested dictionary mapping dinucleotide pairs
    to their stacking free energies in kcal/mol at 37°C.

    Returns:
        A dict where keys are dinucleotide strings (e.g., 'AA', 'GC')
        and values are dicts mapping base-pair contexts to stacking energies.
    """
    stacking_model = {
        'AA': {
            'AA': -0.93, 'AU': -0.88, 'AG': -0.58, 'AC': -0.52,
            'UA': -0.93, 'UU': -0.80, 'UG': -0.50, 'UC': -0.46,
            'GA': -0.59, 'GU': -0.50, 'GG': -0.29, 'GC': -0.12,
            'CA': -0.56, 'CU': -0.48, 'CG': -0.32, 'CC': -0.29
        },
        'AU': {
            'AA': -0.95, 'AU': -0.84, 'AG': -0.64, 'AC': -0.52,
            'UA': -0.95, 'UU': -0.79, 'UG': -0.61, 'UC': -0.47,
            'GA': -0.65, 'GU': -0.60, 'GG': -0.47, 'GC': -0.32,
            'CA': -0.62, 'CU': -0.55, 'CG': -0.48, 'CC': -0.35
        },
        'AG': {
            'AA': -0.89, 'AU': -0.84, 'AG': -0.56, 'AC': -0.51,
            'UA': -0.89, 'UU': -0.78, 'UG': -0.48, 'UC': -0.44,
            'GA': -0.57, 'GU': -0.48, 'GG': -0.27, 'GC': -0.10,
            'CA': -0.54, 'CU': -0.46, 'CG': -0.30, 'CC': -0.27
        },
        'AC': {
            'AA': -0.89, 'AU': -0.80, 'AG': -0.54, 'AC': -0.44,
            'UA': -0.89, 'UU': -0.73, 'UG': -0.44, 'UC': -0.35,
            'GA': -0.55, 'GU': -0.44, 'GG': -0.22, 'GC': -0.04,
            'CA': -0.52, 'CU': -0.42, 'CG': -0.24, 'CC': -0.14
        }
    }
    return stacking_model