update_v3_physics.py

import re

# Read the physics detector
with open('physics_region_detector.py', 'r') as f:
    physics_code = f.read()

# Read v3
with open('quantify_all_metabolites_v3_physics.py', 'r') as f:
    v3_code = f.read()

# Add import and physics functions after the existing imports
import_section_end = v3_code.find("def read_and_process")

physics_functions = '''
# Import physics-based region detection
import sys
sys.path.insert(0, '.')
from physics_region_detector import (
    group_expected_peaks, 
    detect_actual_region,
    get_physics_based_regions,
    METABOLITE_PHYSICS
)

'''

v3_code = v3_code[:import_section_end] + physics_functions + v3_code[import_section_end:]

# Replace the metabolite info function
old_func_start = v3_code.find("def get_metabolite_info_v3()")
old_func_end = v3_code.find("def fit_region", old_func_start)

new_func = '''def get_metabolite_info_v3():
    """
    Return metabolite information with physics-based expected peak positions.
    
    Actual regions are detected automatically from spectra using physics principles:
    - PURE-SHIFT NMR: Each distinct group → 1 singlet
    - DIASTEREOTOPIC: CH2 next to chiral center → 2 peaks  
    - REGION GROUPING: Peaks within 0.3 ppm grouped together
    - BOUNDARIES: Auto-detected at 10% peak height
    """
    return METABOLITE_PHYSICS

def get_detected_regions_for_metabolite(met_name, ppm, intensity):
    """Get physics-based detected regions for a specific metabolite."""
    if met_name not in METABOLITE_PHYSICS:
        return None
    
    expected = METABOLITE_PHYSICS[met_name]
    regions = get_physics_based_regions(met_name, ppm, intensity, expected)
    
    # Convert to format expected by fitting code
    result = {
        'regions': [r['bounds'] for r in regions],
        'region_peaks': [r['peaks'] for r in regions],
        'region_protons': [r['protons'] for r in regions],
        'region_names': [r['name'] for r in regions],
    }
    
    return result, regions

'''

v3_code = v3_code[:old_func_start] + new_func + v3_code[old_func_end:]

# Write updated file
with open('quantify_all_metabolites_v3_physics.py', 'w') as f:
    f.write(v3_code)

print("Updated quantify_all_metabolites_v3_physics.py with physics-based region detection")