remove_hydrogens.py

import sys

def remove_hydrogen_atoms(pdb_file_path, output_dir):
    output_file_path = output_dir + pdb_file_path.replace('.pdb', '_no_hydrogen.pdb')
    
    with open(pdb_file_path, 'r') as pdb_file, open(output_file_path, 'w') as output_file:
        for line in pdb_file:
            if line.startswith("ATOM") or line.startswith("HETATM"):
                atom_name = line[12:16].strip()  # Atom name field
                if atom_name[0] == 'H':
                    continue  # Skip hydrogen atoms
            output_file.write(line)
    
    print(f"Output file saved to: {output_file_path}")

if __name__ == "__main__":
    if len(sys.argv) != 3:
        print("Usage: python script.py <pdb_file_path> <output_dir>")
        sys.exit(1)
    
    pdb_file_path = sys.argv[1]
    output_dir = sys.argv[2]
    remove_hydrogen_atoms(pdb_file_path, output_dir)