Create pdbfix.py

utils/pdbfix.py

@@ -0,0 +1,23 @@
+import os
+import glob
+from pdbfixer import PDBFixer
+from openmm.app import PDBFile
+
+base_dir = 'posebusters_benchmark_set'
+suffix = '_protein.pdb'
+new_suffix = '_protein_fix.pdb'
+for in_file in list(glob.glob(f'posebusters_benchmark_set/*/*{suffix}')):
+    prefix = os.path.basename(in_file).removesuffix(suffix)
+    out_file = os.path.join(os.path.dirname(in_file), prefix + new_suffix)
+    print(f'{in_file} -> {out_file}')
+
+    fixer = PDBFixer(filename=in_file)
+    fixer.findMissingResidues()
+    fixer.findNonstandardResidues()
+    fixer.replaceNonstandardResidues()
+    # fixer.removeHeterogens(True)
+    fixer.findMissingAtoms()
+    fixer.addMissingAtoms()
+
+    with open(out_file, 'w+') as out:
+        PDBFile.writeFile(fixer.topology, fixer.positions, out)