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Author: O3PS

simple_docking/MTH_Docking_Part2_Dock-Vina_2.0.ipynb

@@ -96,7 +96,7 @@
     "#This defines our receptor structures (all of these files happen to have the same prefix, the starting structure (xal structure) is xxx_00.pdb)\n",
     "receptor_filenames = glob('../receptor/*.pdb')\n",
     "#This defines where the ligand files are found\n",
-    "ligand_filenames = glob('../compounds/Minifrag/*.pdbqt')\n",
+    "ligand_filenames = glob('/home/geoff/compounds/FtsZ/pharmit/pocket3/*.pdbqt')\n",
     "\n",
     "#The sort command is *really* important for organising the output in the right order (the protein files are mixed up otherwise)\n",
     "receptor_filenames.sort()\n",
@@ -112,8 +112,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Number of processors\n",
-    "This tells us about how many processors we have available..."
+    "### Number of processors and number of docking steps per processor\n",
+    "This tells us about how many processors we have available (or lets us set that number) and helps us to get an estimate of how long the this step of the Molecular Treasure Hunt will take to run. Larger molecules are slower to dock (e.g the FDA library compared to fragment libraries) because they have more rotatable bonds. But the number of docking steps per cpu will give a rough guide to how long the docking will take."
    ]
   },
   {
@@ -128,7 +128,12 @@
     "#by commenting out the top line (by adding a # at the start of the line)\n",
     "#and uncommenting the line below (by removing the # from the line) using a number you chose.\n",
     "#only one of the two lines (EITHER the top or the bottom one) should be uncommented.\n",
-    "#num_cpu = 4"
+    "#num_cpu = 4\n",
+    "\n",
+    "docking_steps = len(ligand_filenames) * len(receptor_filenames)\n",
+    "print(\"Number of individual docking_steps is\", docking_steps)\n",
+    "docking_steps_per_cpu = round((docking_steps / num_cpu), 2)\n",
+    "print(\"Number of docking steps per cpu is \", docking_steps_per_cpu)"
    ]
   },
   {
@@ -184,25 +189,6 @@
     "print(colored('Finished making pdbqt files', 'blue', attrs=['bold']))"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "And here we get an estimate of how long the this step of the Molecular Treasure Hunt will take to run. Larger molecules are slower to dock (e.g the FDA library compared to fragment libraries) because they have more rotatable bonds. But the number of docking steps per cpu will give a rough guide to how long the docking will take."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "docking_steps = len(ligand_filenames) * len(receptor_filenames)\n",
-    "print(\"Number of individual docking_steps is\", docking_steps)\n",
-    "docking_steps_per_cpu = round((docking_steps / num_cpu), 2)\n",
-    "print(\"Number of docking steps per cpu is \", docking_steps_per_cpu)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},