import os
os.chdir('/home/allaun/Documents/Research Stack/3-Mathematical-Models')

with open('pist_biological_polymorphic_shifter_v3_complete.py', 'r') as f:
    content = f.read()

# The SBOX is corrupted with duplicate values (0x6d, 0x6c appear multiple times).
# Replace with correct AES S-Box
correct_sbox = [
    0x63,0x7c,0x77,0x7b,0xf2,0x6b,0x6f,0xc5,0x30,0x01,0x67,0x2b,0xfe,0xd7,0xab,0x76,
    0xca,0x82,0xc9,0x7d,0xfa,0x59,0x47,0xf0,0xad,0xd4,0xa2,0xaf,0x9c,0xa4,0x72,0xc0,
    0xb7,0xfd,0x93,0x26,0x36,0x3f,0xf7,0xcc,0x34,0xa5,0xe5,0xf1,0x71,0xd8,0x31,0x15,
    0x04,0xc7,0x23,0xc3,0x18,0x96,0x05,0x9a,0x07,0x12,0x80,0xe2,0xeb,0x27,0xb2,0x75,
    0x09,0x83,0x2c,0x1a,0x1b,0x6e,0x5a,0xa0,0x52,0x3b,0xd6,0xb3,0x29,0xe3,0x2f,0x84,
    0x53,0xd1,0x00,0xed,0x20,0xfc,0xb1,0x5b,0x6a,0xcb,0xbe,0x39,0x4a,0x4c,0x58,0xcf,
    0xd0,0xef,0xaa,0xfb,0x43,0x4d,0x33,0x85,0x45,0xf9,0x02,0x7f,0x50,0x3c,0x9f,0xa8,
    0x51,0xa3,0x40,0x8f,0x92,0x9d,0x38,0xf5,0xbc,0xb6,0xda,0x21,0x10,0xff,0xf3,0xd2,
    0xcd,0x0c,0x13,0xec,0x5f,0x97,0x44,0x17,0xc4,0xa7,0x7e,0x3d,0x64,0x5d,0x19,0x73,
    0x60,0x81,0x4f,0xdc,0x22,0x2a,0x90,0x88,0x46,0xee,0xb8,0x14,0xde,0x5e,0x0b,0xdb,
    0xe0,0x32,0x3a,0x0a,0x49,0x06,0x24,0x5c,0xc2,0xd3,0xac,0x62,0x91,0x95,0xe4,0x79,
    0xe7,0xc8,0x37,0x6d,0x8d,0xd5,0x4e,0xa9,0x6c,0x56,0xf4,0xea,0x65,0x7a,0xae,0x08,
    0xba,0x78,0x25,0x2e,0x1c,0xa6,0xb4,0xc6,0xe8,0xdd,0x74,0x1f,0x4b,0xbd,0x8b,0x8a,
    0x70,0x3e,0xb5,0x66,0x48,0x03,0xf6,0x0e,0x61,0x35,0x57,0xb9,0x86,0xc1,0x1d,0x9e,
    0xe1,0xf8,0x98,0x11,0x69,0xd9,0x8e,0x94,0x9b,0x1e,0x87,0xe9,0xce,0x55,0x28,0xdf,
    0x8c,0xa1,0x89,0x0d,0xbf,0xe6,0x42,0x68,0x41,0x99,0x2d,0x0f,0xb0,0x54,0xbb,0x16,
]

# Find and replace the SBOX definition
# The current SBOX starts at a specific line. Let's find it.
old_start = "    SBOX = ["
old_end = "    ]"

# Find the SBOX definition
idx_start = content.find("    SBOX = [")
if idx_start > 0:
    idx_end = content.find("\n    # Inverse S-Box", idx_start)
    if idx_end > idx_start:
        # Build replacement
        sbox_lines = "    SBOX = [\n"
        for i in range(0, 256, 16):
            chunk = correct_sbox[i:i+16]
            hex_vals = ",".join(f"0x{v:02x}" for v in chunk)
            sbox_lines += f"        {hex_vals},\n"
        sbox_lines += "    ]"

        old_sbox_block = content[idx_start:idx_end]
        content = content[:idx_start] + sbox_lines + content[idx_end:]
        print("SBOX replaced with correct AES S-Box")
    else:
        print("Could not find end of SBOX definition")
else:
    print("Could not find SBOX definition")

with open('pist_biological_polymorphic_shifter_v3_complete.py', 'w') as f:
    f.write(content)

# Verify no duplicates
s = set()
has_dup = False
for v in correct_sbox:
    if v in s:
        print(f"DUPLICATE: {v}")
        has_dup = True
    s.add(v)
if not has_dup:
    print("SBOX has all unique values (bijection confirmed)")
print("Length:", len(content))