| from pdbfixer import PDBFixer | |
| from openmm.app import PDBFile | |
| # Load the PDB file | |
| fixer = PDBFixer(filename='your_file.pdb') | |
| # Find missing residues | |
| fixer.findMissingResidues() | |
| # Replace nonstandard residues | |
| fixer.findNonstandardResidues() | |
| fixer.replaceNonstandardResidues() | |
| # Find missing atoms and add them | |
| fixer.findMissingAtoms() | |
| fixer.addMissingAtoms() | |
| # Write the fixed PDB file | |
| PDBFile.writeFile(fixer.topology, fixer.positions, open('fixed_pdb.pdb', 'w')) |