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AutodockPDB.py

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+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# My first example with AutoDock Vina in python
+#
+import os
+import subprocess
+import timeout_decorator
+from vina import Vina
+
+
+v = Vina(sf_name='vina', cpu = 6, seed = 12345)
+
+# v.set_receptor('/Users/yashravipati/Downloads/PDBBind_processed/1a4g/1a4g_protein_processed.pdb.pdbqt')
+
+# v.set_ligand_from_file('/Users/yashravipati/Downloads/PDBBind_processed/1a4g/1a4g_ligand.mol2.pdbqt')
+# v.compute_vina_maps(center=[15.190, 53.903, 16.917], box_size=[20, 20, 20])
+
+@timeout_decorator.timeout(5)
+def dock_vina(receptor_file, ligand_file):
+    v.set_receptor(receptor_file)
+    v.set_ligand_from_file(ligand_file)
+    v.compute_vina_maps(center=[15.190, 53.903, 16.917], box_size=[20, 20, 20])
+    v.dock(exhaustiveness=32, n_poses=20)
+    v.write_poses(ligand_file[:-5] + "_docked.pdbqt", n_poses=5, overwrite=True)
+
+root_dir = "/Users/yashravipati/Downloads/PDBBind_processed"
+
+x = 0
+for dirpath, dirnames, filenames in os.walk(root_dir):
+    for filename in filenames:
+        if filename.endswith(".pdbqt"):
+            # Check if the file is a receptor or a ligand
+            if "protein" in filename:
+                receptor_file = os.path.join(dirpath, filename)
+                x += 1
+            elif "ligand" in filename:
+                ligand_file = os.path.join(dirpath, filename)
+                x += 1
+                # Dock the receptor and ligand
+            if x == 2:
+                print(receptor_file + "\n" + ligand_file) 
+                x=0
+                try:
+                    dock_vina(receptor_file, ligand_file)
+                except timeout_decorator.timeout_decorator.TimeoutError:
+                    print("Skipping iteration as it took too long")
+                    continue  # move on to the next iteration