Add option to write vina-style fridbox text file

meeko/gridbox.py

@@ -150,5 +150,11 @@ def calc_box(coord_array, padding):
     size_z = z_max - z_min + 2 * padding
     return (center_x, center_y, center_z), (size_x, size_y, size_z)
 
+def box_to_vina_string(gridcenter, gridsizes):
+    dims = ['x', 'y', 'z']
+    centers_str = "\n".join([f"center_{d} = {gridcenter[i]}" for i, d in enumerate(dims)])
+    sizes_str = "\n".join([f"size_{d} = {gridsizes[i]}" for i, d in enumerate(dims)])
+    return centers_str + "\n" + sizes_str
+
 boron_silicon_atompar  = "atom_par Si     4.10  0.200  35.8235  -0.00143  0.0  0.0  0  -1  -1  6" + os_linesep
 boron_silicon_atompar += "atom_par B      3.84  0.155  29.6478  -0.00152  0.0  0.0  0  -1  -1  0" + os_linesep

scripts/mk_prepare_receptor.py

@@ -154,6 +154,7 @@ def get_args():
     box_group.add_argument('--box_center_on_reactive_res', help="project center of grid box along CA-CB bond 5 A away from CB", action="store_true")
     box_group.add_argument('--ligand', help="Reference ligand file path: .sdf, .mol, .mol2, .pdb, and .pdbqt files accepted")
     box_group.add_argument('--padding', help="padding around reference ligand [A]", type=float)
+    box_group.add_argument('--write_vinabox', help='Write vina-style gridbox file', action='store_true')
 
 
     #reactive_group = parser.add_argument_group("Reactive")
@@ -471,6 +472,14 @@ def get_args():
     with open(box_fn, "w") as f:
         f.write(gridbox.box_to_pdb_string(box_center, npts))
 
+    # write gridbox vina format
+    if args.write_vinabox:
+        box_vina_fn = pathlib.Path(rigid_fn).with_suffix("_box.txt")
+        written_files_log["filename"].append(box_vina_fn)
+        written_files_log["description"].append("Vina-style box dimension file")
+        with open(box_vina_fn, "w") as f:
+            f.write(gridbox.box_to_vina_string(box_center, box_size))
+
     # check all flexres are inside the box
     if len(reactive_flexres) > 0:
         any_outside = False