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Author: O3PS

simple_docking/MTH_Docking_Part2_Dock-Vina_2.0.ipynb

@@ -180,10 +180,9 @@
     "#Let's use oddt to make the pdbqt files that we need...\n",
     "print(colored('Making pdbqt files', 'blue', attrs=['bold']))\n",
     "for receptor_filename in receptor_filenames:\n",
-    "    receptor_prefix = receptor_filename.split(\".\")[2]\n",
-    "    receptor_name = receptor_prefix.split(\"/\")[2]\n",
-    "    receptor_pdbqt_file = '..' + receptor_prefix + '.pdbqt'\n",
-    "    print(receptor_name)\n",
+    "    receptor_prefix = receptor_filename.removesuffix('.pdb')\n",
+    "    receptor_name = receptor_prefix.split(\"/\")[-1]\n",
+    "    receptor_pdbqt_file = receptor_prefix + '.pdbqt'\n",
     "    rec = next(oddt.toolkit.readfile('pdb', receptor_filename))\n",
     "    rec.write('pdbqt', receptor_pdbqt_file, overwrite=True, opt={'r': None, 'c': None, 'h': None})\n",
     "print(colored('Finished making pdbqt files', 'blue', attrs=['bold']))"
@@ -204,10 +203,10 @@
    "source": [
     "def dock_ligands(filename):\n",
     "    #This line removes the filename suffix (.pdbqt)\n",
-    "    dock_input = filename.split(\".\")[0]\n",
+    "    dock_input = filename.removesuffix('.pdbqt')\n",
     "    #This line removes the filename prefix \n",
     "    dock_name = dock_input.split(\"/\")[-1]\n",
-    "    vina_receptor = '..' + PDBFile + '.pdbqt'\n",
+    "    vina_receptor = PDBFile + '.pdbqt'\n",
     "    vina_config = \"../receptor/conf.txt\"\n",
     "    vina_ligand = dock_input + '.pdbqt'\n",
     "    vina_out = dock_name + '_out.pdbqt'\n",
@@ -232,7 +231,7 @@
     "        top_pose = next(oddt.toolkit.readfile('pdbqt', dock_name + '_out.pdbqt'))\n",
     "        top_pose_out = top_pose.write('mol2')\n",
     "        mol = top_pose\n",
-    "        protein = '..' + PDBFile + '.pdb'\n",
+    "        protein = PDBFile + '.pdb'\n",
     "        rec = next(oddt.toolkit.readfile('pdb', protein))\n",
     "        rec.protein=True\n",
     "        mols = list(oddt.toolkit.readfile('mol2', filename))\n",
@@ -294,13 +293,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "#This runs a series of docking calculations on protein conformations found in the receptor folder\n",
     "for receptor_filename in receptor_filenames:\n",
-    "    PDBFile = receptor_filename.split(\".\")[2]\n",
-    "    PDBFile_name = PDBFile.split(\"/\")[2]\n",
+    "    PDBFile = receptor_filename.removesuffix('.pdb')\n",
+    "    PDBFile_name = PDBFile.split(\"/\")[-1]\n",
     "    print(colored('Docking for protein started', 'blue', attrs=['bold']))\n",
     "    print(PDBFile_name)\n",
     "   \n",

simple_docking/MTH_Docking_Part3_Analysis_2.0.ipynb

@@ -511,7 +511,7 @@
    "source": [
     "# Draw Violin Plot\n",
     "plt.figure(figsize=(13,10), dpi= 80)\n",
-    "sns.violinplot(x='Protein_Conf', y='Vina_BE', data=total_dataframes, scale='width', inner='quartile')\n",
+    "sns.violinplot(x='Protein_Conf', y='Vina_BE', data=total_dataframes, density_norm='width', inner='quartile')\n",
     "\n",
     "# Decoration\n",
     "plt.title('Violin Plot of Vina_BE by Protein Conformation', fontsize=22)\n",

simple_docking/MTH_Docking_Part4_Selecting_Hits_2.0.ipynb

@@ -175,7 +175,7 @@
    "outputs": [],
    "source": [
     "sort_by_Ligand_Name = total_dataframes.sort_values('Ligand_Name')\n",
-    "Vina_BE_HBonds_best_overall = sort_by_Ligand_Name[(sort_by_Ligand_Name.Vina_BE < -5.2) & (sort_by_Ligand_Name.HBonds > 0) & (sort_by_Ligand_Name.Vina_LE < -0.4)]\n",
+    "Vina_BE_HBonds_best_overall = sort_by_Ligand_Name[(sort_by_Ligand_Name.Vina_BE < -4.5) & (sort_by_Ligand_Name.HBonds > 0) & (sort_by_Ligand_Name.Vina_LE < -0.4)]\n",
     "Vina_BE_HBonds_best_overall"
    ]
   },
@@ -202,7 +202,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "selection_set = Vina_BE_HBonds_best_overall\n",

simple_docking/MTH_Docking_Part5_Saving_Hits_2.0.ipynb

@@ -95,7 +95,7 @@
     "f.close()\n",
     "for path_results_filename in path_results_filenames:\n",
     "    results_filename=path_results_filename.split('/')[-1]\n",
-    "    results_filename_prefix=results_filename.split('.')[0]\n",
+    "    results_filename_prefix=results_filename.removesuffix('.mol2')\n",
     "    protein=results_filename_prefix.split('_')[1]\n",
     "    all_mols = list(oddt.toolkit.readfile('mol2', path_results_filename))\n",
     "    hits_out_filename=hits_folder + '/' + results_filename_prefix + '_hit_ligands.mol2'\n",
@@ -136,7 +136,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "#Here we write out the files to the MTH_Protein_Hits folder\n",
@@ -151,7 +153,7 @@
     "            with open(protein_hits_out_filename, 'a') as contents:\n",
     "                for path_results_filename in path_results_filenames:\n",
     "                    results_filename=path_results_filename.split('/')[-1]\n",
-    "                    results_filename_prefix=results_filename.split('.')[0]\n",
+    "                    results_filename_prefix=results_filename.removesuffix('.mol2')\n",
     "                    protein_suffix=results_filename_prefix.split('VinaResults_')[1]\n",
     "                    protein=protein_suffix.split('_rescored')[0]\n",
     "                    print(protein)\n",
@@ -199,7 +201,7 @@
     "#Write sdf files for use in DataWarrior etc.\n",
     "mol2_files = glob('MTH_Hits/VinaResults_*.mol2')\n",
     "for mol2_file in mol2_files:\n",
-    "    mol2_prefix = mol2_file.split(\".\")[0]\n",
+    "    mol2_prefix = mol2_file.removesuffix('.mol2')\n",
     "    sdf_out = mol2_prefix + '.sdf'\n",
     "    mols = list(oddt.toolkit.readfile('mol2', mol2_file))\n",
     "    with open (sdf_out, 'w') as contents:\n",