swap_chain_A_B.py

def swap_and_relabel_chains(input_pdb_path, output_pdb_path):
    chain_a_atoms = []
    chain_b_atoms = []
    other_lines = []

    # Read the PDB file and segregate lines based on chain A, chain B, and others
    with open(input_pdb_path, 'r') as pdb_file:
        for line in pdb_file:
            if line.startswith('ATOM'):
                chain_id = line[21]  # Chain identifier is at column 22 (0-based indexing)
                if chain_id == 'A':
                    chain_a_atoms.append(line)
                elif chain_id == 'B':
                    chain_b_atoms.append(line)
                else:
                    other_lines.append(line)
            else:
                other_lines.append(line)

    # Swap chain identifiers: A -> B and B -> A
    swapped_chain_a_atoms = [atom[:21] + 'B' + atom[22:] for atom in chain_a_atoms]
    swapped_chain_b_atoms = [atom[:21] + 'A' + atom[22:] for atom in chain_b_atoms]

    # Combine swapped chains and other lines, with chain B atoms first
    modified_lines = swapped_chain_b_atoms + swapped_chain_a_atoms + other_lines

    # Write the modified content to a new PDB file
    with open(output_pdb_path, 'w') as output_pdb:
        for line in modified_lines:
            output_pdb.write(line)

# Example usage
input_pdb_path = './experimental_structures/exp_6bgg.pdb'  # Replace with your input PDB file path
output_pdb_path = './6bgg.pdb'  # Desired output file path
swap_and_relabel_chains(input_pdb_path, output_pdb_path)