When PT touches the living

# verify_rna_bifurcation.py
# Verify the q⁺/q⁻ bifurcation on an RNA sequence

from pt_protein.bifurcation import compute_q_plus, compute_q_minus
from pt_protein.rna import load_sequence, modular_projection

seq = load_sequence("path/to/rna_sample.fasta")
mu = 4  # |V_4| = 4 for nucleotide bases

q_plus = compute_q_plus(mu)        # 1 - 2/μ
q_minus = compute_q_minus(mu)      # exp(-1/μ)
L = q_minus - q_plus               # latent heat

print(f"q⁺ = {q_plus:.6f}")        # 0.500000  (1 - 2/4)
print(f"q⁻ = {q_minus:.6f}")       # 0.778801  (e^(-1/4))
print(f"L  = {L:.6f}")             # 0.278801

proj_plus = modular_projection(seq, q_plus)
proj_minus = modular_projection(seq, q_minus)

from pt_protein.metrics import dssr_strict_f1
print(f"DSSR F1 = {dssr_strict_f1(proj_plus, proj_minus, seq):.3f}")
# expected: ~0.958 on the internal corpus

# allostery_shuffle_test.py
# Crucial test: does the PT signal survive a residue shuffle?

from pt_protein.allostery import compute_pt_signal, shuffle_residues
import numpy as np

protein_pdb = "1AVI.pdb"  # Avidin, known allosteric
n_perm = 1000

signal_real = compute_pt_signal(protein_pdb)
signals_shuffled = [
    compute_pt_signal(shuffle_residues(protein_pdb, seed=i))
    for i in range(n_perm)
]

p_value = np.mean(np.array(signals_shuffled) >= signal_real)
print(f"real signal : {signal_real:.4f}")
print(f"p-value     : {p_value:.4f}")    # expected: 0.0000 (0/1000)
print(f"verdict     : {'PASS' if p_value < 0.01 else 'FAIL'}")

# ramachandran_torus.py
# Reconstruct the Ramachandran torus from modular projections

from pt_protein.aa import twenty_amino_acids, modular_position

phi_psi = []
for aa in twenty_amino_acids:
    phi, psi = modular_position(aa)  # projection onto Z/(2p)Z
    phi_psi.append((aa, phi, psi))
    print(f"{aa.symbol:3} {aa.name:15} φ={phi:6.1f}° ψ={psi:6.1f}°")

# Comparison with observed basins (Lovell et al. 2003)
from pt_protein.metrics import ramachandran_bin_match
matches = ramachandran_bin_match(phi_psi)
print(f"\n{matches}/20 amino acids in the correct Ramachandran basin")
# expected: 20/20