Add files via upload

suneelbvs · Jan 17, 2020 · 92efd73 · 92efd73
1 parent 9aa1653
commit 92efd73
Showing 1 changed file with 26 additions and 15 deletions.
diff --git a/1_Reading and Writing Smiles using rdKit.ipynb b/1_Reading and Writing Smiles using rdKit.ipynb
@@ -4,18 +4,22 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "# Tutorial -1 \n",
+    "\n",
+    "# File Handling using rdKit\n",
+    "\n",
     "# Reading and Writing Smiles using rdKit\n",
     "\n",
-    "This is a short overview of creating molecules from and writing molecules to various file formats. It is intended to be a complement to, not replacement for, the contents of the [main RDKit documentation](http://rdkit.org/docs/index.html)\n",
+    "This is a short overview of reading, creating smiles from different file types and writing molecules to various file formats. It is intended to be a complement to, not replacement for, the contents of the [main RDKit documentation](http://rdkit.org/docs/index.html)\n",
     "\n",
-    "Material Prepared using : @iwatobipen [https://github.com/iwatobipen];  @rdkit [https://github.com/rdkit]\n",
+    "Credits to @iwatobipen [https://github.com/iwatobipen];  @rdkit [https://github.com/rdkit]\n",
     "\n",
     "@TAGS: #basics #molecule_input #rdKitTutorials #Smiles #CADD"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 117,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -40,12 +44,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If you have a SMILES string, the easiest thing to use is MolFromSmiles:"
+    "Reading a SMILES string using MolFromSmiles:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 59,
+   "execution_count": 2,
    "metadata": {
     "scrolled": true
    },
@@ -54,10 +58,10 @@
      "data": {
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\n",
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x1ffbde625d0>"
+       "<rdkit.Chem.rdchem.Mol at 0x2046601a5d0>"
       ]
      },
-     "execution_count": 59,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -69,7 +73,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 60,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -140,6 +144,13 @@
     "print(Chem.MolToMolBlock(m2))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Adjusting Hydrogens and removing them"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 61,
@@ -193,38 +204,38 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note that the coordinates used for the drawing are not present in the molecule, the RDKit generates them when the molecule is drawn."
+    "Writing molecules in SD and SMI formats"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 79,
+   "execution_count": 189,
    "metadata": {},
    "outputs": [],
    "source": [
-    "w1 = Chem.SDWriter('data_set.sdf')\n",
+    "w1 = Chem.SDWriter('./data/data_set.sdf')\n",
     "w1.write(mol_exampleH)\n",
     "w1.close()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 97,
+   "execution_count": 190,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "<rdkit.Chem.rdmolfiles.SmilesMolSupplier object at 0x000001FFBDE67CE0>\n"
+      "<rdkit.Chem.rdmolfiles.SmilesMolSupplier object at 0x000001FFC02480D8>\n"
      ]
     }
    ],
    "source": [
-    "w2 = Chem.SmilesWriter('data_set.smi')\n",
+    "w2 = Chem.SmilesWriter('./data/data_set.smi')\n",
     "w2.write(mol_exampleH)\n",
     "w2.close()\n",
-    "s1 = Chem.SmilesMolSupplier('data_set.smi')\n",
+    "s1 = Chem.SmilesMolSupplier('./data/data_set.smi')\n",
     "print(s1)"
    ]
   },