v1.2.2

Author: RyanZR

notebooks/basic_molecular_docking.ipynb

@@ -221,7 +221,7 @@
         "    zcoor = [molConf.GetAtomPosition(c).z for c in range(len(molAtom))]\n",
         "    return [xcoor, ycoor, zcoor]\n",
         "\n",
-        "def labogrid(coorList, scale=2):\n",
+        "def labox(coorList, scale=2):\n",
         "    X, Y, Z = coorList[0], coorList[1], coorList[2]\n",
         "    range = [[min(X), max(X)],\n",
         "             [min(Y), max(Y)],\n",
@@ -304,7 +304,7 @@
         "            columns=INTER[BSI_key][BD_key][0])\n",
         "        if not DF.empty:\n",
         "            INTER_TYPE.extend([BD_key.upper()]*len(DF))\n",
-        "            INTER_DF = INTER_DF.append(DF)\n",
+        "            INTER_DF = pd.concat([INTER_DF, DF], ignore_index=True)\n",
         "    INTER_DF = INTER_DF.assign(BOND=INTER_TYPE)\n",
         "    INTER_DF.reset_index(drop=True, inplace=True)\n",
         "    INTER_DF.to_csv(CSV_Ifile, index=False)\n",
@@ -382,7 +382,7 @@
         "              showChain=False, showResLabel=False, showVDW=False,\n",
         "              outline=False):\n",
         "    # Variables\n",
-        "    mview = py3Dmol.view(1000,1500)\n",
+        "    mview = py3Dmol.view(width=960, height=640)\n",
         "    if model in \"none\":\n",
         "        model = cType = color = \"\"\n",
         "    if model in \"cartoon\":\n",
@@ -391,7 +391,7 @@
         "        cType, color = \"colorscheme\", color + \"Carbon\"\n",
         "\n",
         "    # Protein Model\n",
-        "    count = 1\n",
+        "    count = 0\n",
         "    prot_model = count\n",
         "    print(f\"+ Showing {os.path.basename(inputP)}\")\n",
         "    mol = open(inputP, \"r\").read()\n",
@@ -451,10 +451,10 @@
         "\n",
         "def VIEW_ELIG(inputE, showAtomLabel=False, outline=False):\n",
         "    # Variable\n",
-        "    mview = py3Dmol.view(1000, 1500)\n",
+        "    mview = py3Dmol.view(width=960, height=640)\n",
         "\n",
         "    # Experimental ligand model\n",
-        "    count = 1\n",
+        "    count = 0\n",
         "    elig_model = count\n",
         "    print(f\"+ Showing {os.path.basename(inputE)}\")\n",
         "    mol = open(inputE, \"r\").read()\n",
@@ -484,10 +484,10 @@
         "\n",
         "def VIEW_LIG(inputL, showHs=False, showAtomLabel=False, outline=False):\n",
         "    # Variable\n",
-        "    mview = py3Dmol.view(1000, 1500)\n",
+        "    mview = py3Dmol.view(width=960, height=640)\n",
         "\n",
         "    # Ligand model\n",
-        "    count = 1\n",
+        "    count = 0\n",
         "    lig_model = count\n",
         "    print(f\"+ Showing {os.path.basename(inputL)}\")\n",
         "    smi = open(inputL, \"r\").read()\n",
@@ -525,7 +525,7 @@
         "\n",
         "def VIEW_GRID(inputP, inputE, focusRes, center, size=[10, 10, 10]):\n",
         "    # Variable\n",
-        "    mview = py3Dmol.view(1000, 1500)\n",
+        "    mview = py3Dmol.view(width=960, height=640)\n",
         "\n",
         "    # Grid box\n",
         "    bxi, byi, bzi = center[0], center[1], center[2]\n",
@@ -538,7 +538,7 @@
         "        \"color\": \"skyBlue\", \"opacity\": 0.7})\n",
         "\n",
         "    # Protein model\n",
-        "    count = 1\n",
+        "    count = 0\n",
         "    prot_model = count\n",
         "    print(f\"+ Showing {os.path.basename(inputP)}\")\n",
         "    molA = open(inputP, \"r\").read()\n",
@@ -585,7 +585,7 @@
         "              showLig=False, showAllPose=False, showBestPose=False,\n",
         "              outline=False):\n",
         "    # Variables\n",
-        "    mview = py3Dmol.view(1000,1500)\n",
+        "    mview = py3Dmol.view(width=960, height=640)\n",
         "    if model in \"none\":\n",
         "        model = cType = color = \"\"\n",
         "    if model in \"cartoon\":\n",
@@ -594,7 +594,7 @@
         "        cType, color = \"colorscheme\", color + \"Carbon\"\n",
         "\n",
         "    # Protein model\n",
-        "    count = 1\n",
+        "    count = 0\n",
         "    prot_model = count\n",
         "    print(f\"+ Showing {os.path.basename(inputP)}\")\n",
         "    molA = open(inputP, \"r\").read()\n",
@@ -1098,13 +1098,13 @@
         "#@markdown Place the **< Gridbox >** at the center of binding site. \\\n",
         "\n",
         "Focus_residues = \"\" #@param {type:\"string\"}\n",
-        "Method = \"LABOGRID\" #@param [\"LABOGRID\", \"eBoxSize\", \"eBoxSize-modified\", \"Autodock-Grid\", \"manual\"]\n",
+        "Method = \"LaBOX\" #@param [\"LaBOX\", \"eBoxSize\", \"eBoxSize-modified\", \"Autodock-Grid\", \"manual\"]\n",
         "\n",
         "#@markdown ---\n",
         "\n",
-        "if Method == \"LABOGRID\":\n",
+        "if Method == \"LaBOX\":\n",
         "    atomCoord = get_atom_coordinate(EXP_pdb_Dfile)\n",
-        "    grid = labogrid(atomCoord)\n",
+        "    grid = labox(atomCoord)\n",
         "    Center, Size = grid[0], grid[1]\n",
         "\n",
         "if Method == \"eBoxSize\":\n",
@@ -1398,7 +1398,7 @@
       "source": [
         "#@title **Show interaction profile of ligand** {run: \"auto\"}\n",
         "\n",
-        "Select_ligand = \"C26A6_2\" #@param {type : \"string\"}\n",
+        "Select_ligand = \"C26A6_1\" #@param {type : \"string\"}\n",
         "LIG_inter_CSV_Ifile = os.path.join(INT_FLD, f\"{Select_ligand[:-2]}/{Select_ligand}_inter.csv\")\n",
         "view_interaction(LIG_inter_CSV_Ifile, result=\"summary\")"
       ],
@@ -1549,7 +1549,7 @@
       ],
       "provenance": [],
       "mount_file_id": "1jj_nqfJuwJhZyR3x8vpiddRd-EWsuQVr",
-      "authorship_tag": "ABX9TyOZmzKPcYq9ca4Vc0dM6ZFN",
+      "authorship_tag": "ABX9TyOJ7aq4YTm/SBv+Dyg23ETy",
       "include_colab_link": true
     },
     "kernelspec": {