Generate gpf with all atoms

Author: DaniDelHoyo

autodock/protocols/protocol_autoLigand.py

@@ -158,7 +158,7 @@ def generateGridStep(self):
             npts = (radius * 2) / self.spacing.get()
 
             makePath(outDir)
-            gpfFile = generate_gpf(self.getReceptorPDBQT(), spacing=self.spacing.get(),
+            gpfFile = generate_gpf(self.getReceptorPDBQT(), spacing=self.spacing.get(), allDefAtomTypes=True,
                                     xc=xCenter, yc=yCenter, zc=zCenter,
                                     npts=npts, outDir=outDir)
 

autodock/protocols/protocol_autodock_score.py

@@ -118,7 +118,7 @@ def generateGridsStep(self):
     makePath(outDir)
 
     npts = (radius * 2) / self.spacing.get()
-    gpf_file = generate_gpf(fnReceptor, spacing=self.spacing.get(),
+    gpf_file = generate_gpf(fnReceptor, spacing=self.spacing.get(), allDefAtomTypes=True,
                             xc=x_center, yc=y_center, zc=z_center,
                             npts=npts, outDir=outDir, ligandFns=self.ligandFileNames)
 

autodock/protocols/protocol_dock_vina.py

@@ -110,7 +110,7 @@ def dockStep(self, it, pocket=None):
 
       znFFfile = autodockPlugin.getPackagePath(package='VINA', path='AutoDock-Vina/data/AD4Zn.dat') \
         if self.doZnDock.get() else None
-      gpfFile = generate_gpf(fnReceptor, spacing=spacing,
+      gpfFile = generate_gpf(fnReceptor, spacing=spacing, allDefAtomTypes=True,
                               xc=xCenter, yc=yCenter, zc=zCenter,
                               npts=npts, outDir=outDir, ligandFns=pdbqtFiles, znFFfile=znFFfile)
 

autodock/protocols/protocol_generate_grid.py

@@ -119,7 +119,7 @@ def prepareGrid(self):
         # Create the GPF file, required by autogrid to build the grid and glg
         npts = (self.radius.get()*2)/self.spacing.get()  # x,y,z points of the grid
 
-        gpfFile = generate_gpf(atomStructFn, spacing=self.spacing.get(),
+        gpfFile = generate_gpf(atomStructFn, spacing=self.spacing.get(), allDefAtomTypes=True,
                                      xc=xCenter, yc=yCenter, zc=zCenter,
                                      npts=npts, outDir=self._getExtraPath())