looking at the data.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "aad06c61",
   "metadata": {},
   "source": [
    "# Look at some compounds from PubChem Substance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "8c00690f",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2021.03.1\n"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "import rdkit\n",
    "print(rdkit.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "599d9597",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 6 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 6 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 17 H, 2, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 7 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 11 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 17 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 9 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 6 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 6 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 6 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 4 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 24 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 24 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 24 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 24 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 14 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 15 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 14 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 17 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 17 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 15 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 21 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 21 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 14 In, 7, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 40 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 21 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 26 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 50 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 40 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 2 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 2 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 1 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 4 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 17 C, 5, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 17 C, 5, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 11 C, 5, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 1 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 4 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 8 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 6 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 6 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:34:30] Explicit valence for atom # 6 O, 3, is greater than permitted\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "101"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import gzip\n",
    "with gzip.open('/home/glandrum/T5/Data/Pubchem/Substance_000000001_000500000.sdf.gz') as inf:\n",
    "    supplier = Chem.ForwardSDMolSupplier(inf,sanitize=False)\n",
    "    failed_mols = []\n",
    "    for m in supplier:\n",
    "        cm = Chem.Mol(m)\n",
    "        try:\n",
    "            Chem.SanitizeMol(cm)\n",
    "        except:\n",
    "            failed_mols.append(m)\n",
    "            if len(failed_mols)>100:\n",
    "                break\n",
    "len(failed_mols)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "bb7c5663",
   "metadata": {},
   "outputs": [],
   "source": [
    "cms = [Chem.Mol(m) for m in failed_mols]\n",
    "for cm in cms:\n",
    "    cm.UpdatePropertyCache(strict=False)\n",
    "    Chem.GetSymmSSSR(cm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "503d8c75",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "101"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(cms)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "1233e033",
   "metadata": {},
   "outputs": [
    {
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     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "show_mol(3,cms)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "5b282eac",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "model_id": "c367675d4c9b4f37ac2b40c58075d80e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(Dropdown(description='idx', options=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 1…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from ipywidgets import interact,fixed\n",
    "from rdkit.Chem.Draw import rdMolDraw2D\n",
    "from IPython.display import SVG\n",
    "\n",
    "@interact(idx=range(0,len(cms)),ms=fixed(cms))\n",
    "def show_mol(idx,ms):\n",
    "    d2d = rdMolDraw2D.MolDraw2DSVG(450,400)\n",
    "    d2d.drawOptions().prepareMolsBeforeDrawing=False\n",
    "    d2d.DrawMolecule(ms[idx])\n",
    "    d2d.FinishDrawing()\n",
    "    return SVG(d2d.GetDrawingText())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "5a8d554e",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RDKit ERROR: [15:37:09] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:09] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:09] Explicit valence for atom # 5 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:09] Explicit valence for atom # 2 N, 4, is greater than permitted\n",
      "RDKit WARNING: [15:37:09] Warning: conflicting stereochemistry at atom 20 ignored. by rule 1a.\n",
      "RDKit WARNING: [15:37:09] Warning: conflicting stereochemistry at atom 20 ignored. by rule 1a.\n",
      "RDKit ERROR: [15:37:09] Explicit valence for atom # 0 Cl, 7, is greater than permitted\n",
      "RDKit ERROR: [15:37:10] Explicit valence for atom # 4 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:12] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:14] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:14] Explicit valence for atom # 0 O, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:15] Explicit valence for atom # 0 B, 5, is greater than permitted\n",
      "RDKit ERROR: [15:37:17] Explicit valence for atom # 0 S, 8, is greater than permitted\n",
      "RDKit ERROR: [15:37:17] Explicit valence for atom # 0 S, 8, is greater than permitted\n",
      "RDKit ERROR: [15:37:17] Explicit valence for atom # 1 S, 8, is greater than permitted\n",
      "RDKit ERROR: [15:37:17] Explicit valence for atom # 0 S, 8, is greater than permitted\n",
      "RDKit ERROR: [15:37:18] Explicit valence for atom # 12 B, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:21] Explicit valence for atom # 3 N, 5, is greater than permitted\n",
      "RDKit ERROR: [15:37:23] Explicit valence for atom # 2 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:23] Explicit valence for atom # 2 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:23] Explicit valence for atom # 4 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:23] Explicit valence for atom # 2 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:23] Explicit valence for atom # 4 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:23] Explicit valence for atom # 2 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:23] Explicit valence for atom # 4 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:23] Explicit valence for atom # 2 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:24] Explicit valence for atom # 19 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:24] Explicit valence for atom # 0 C, 6, is greater than permitted\n",
      "RDKit ERROR: [15:37:24] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:25] Explicit valence for atom # 1 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:25] Explicit valence for atom # 1 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:25] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:26] Explicit valence for atom # 1 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:28] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:28] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:28] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:28] Explicit valence for atom # 1 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:30] Explicit valence for atom # 14 B, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:30] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:32] Explicit valence for atom # 1 O, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:34] Explicit valence for atom # 1 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:35] Explicit valence for atom # 2 C, 6, is greater than permitted\n",
      "RDKit WARNING: [15:37:35] Warning: conflicting stereochemistry at atom 19 ignored. by rule 2b.\n",
      "RDKit ERROR: [15:37:35] Explicit valence for atom # 1 C, 5, is greater than permitted\n",
      "RDKit ERROR: [15:37:35] Explicit valence for atom # 5 C, 6, is greater than permitted\n",
      "RDKit ERROR: [15:37:38] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:41] Explicit valence for atom # 3 N, 5, is greater than permitted\n",
      "RDKit ERROR: [15:37:41] Explicit valence for atom # 0 Ca, 6, is greater than permitted\n",
      "RDKit ERROR: [15:37:43] Explicit valence for atom # 1 O, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:43] Explicit valence for atom # 3 O, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:44] Explicit valence for atom # 0 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:44] Explicit valence for atom # 0 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:44] Explicit valence for atom # 0 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:44] Explicit valence for atom # 0 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:44] Explicit valence for atom # 0 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 16 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 0 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 3 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 3 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 6 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 0 Cl, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 11 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 2 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 0 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:45] Explicit valence for atom # 3 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:46] Explicit valence for atom # 4 N, 4, is greater than permitted\n",
      "RDKit ERROR: [15:37:46] Explicit valence for atom # 1 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:46] Explicit valence for atom # 1 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:46] Explicit valence for atom # 2 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:46] Explicit valence for atom # 3 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:46] Explicit valence for atom # 0 Cl, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:46] Explicit valence for atom # 0 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:46] Explicit valence for atom # 0 F, 2, is greater than permitted\n",
      "RDKit ERROR: [15:37:47] Explicit valence for atom # 4 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:47] Explicit valence for atom # 4 O, 3, is greater than permitted\n",
      "RDKit ERROR: [15:37:47] Explicit valence for atom # 6 O, 3, is greater than permitted\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "74"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "badAtoms = Chem.MolFromSmarts('[!$([#1,#3,#11,#19,#4,#12,#20,#5,#6,#14,#7,#15,#8,#16,#9,#17,#35,#53])]')\n",
    "\n",
    "import gzip\n",
    "with gzip.open('/home/glandrum/T5/Data/Pubchem/Substance_000000001_000500000.sdf.gz') as inf:\n",
    "    supplier = Chem.ForwardSDMolSupplier(inf,sanitize=False)\n",
    "    failed_mols = []\n",
    "    for m in supplier:\n",
    "        cm = Chem.Mol(m)\n",
    "        if cm.HasSubstructMatch(badAtoms):\n",
    "            continue\n",
    "        try:\n",
    "            Chem.SanitizeMol(cm)\n",
    "        except:\n",
    "            failed_mols.append(m)\n",
    "            if len(failed_mols)>100:\n",
    "                break\n",
    "len(failed_mols)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "92b3b78f",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RDKit ERROR: [15:42:40] Explicit valence for atom # 1 O, 3, is greater than permitted\n"
     ]
    }
   ],
   "source": [
    "#from rdkit import RDLogging\n",
    "from rdkit import RDLogger\n",
    "RDLogger.EnableLog('rdApp.*')\n",
    "Chem.MolFromSmiles('CO(C)C')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "1d5d6c36",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RDKit WARNING: [15:37:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
      "RDKit WARNING: [15:37:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
      "RDKit WARNING: [15:37:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n"
     ]
    }
   ],
   "source": [
    "cms = [Chem.Mol(m) for m in failed_mols]\n",
    "for cm in cms:\n",
    "    cm.UpdatePropertyCache(strict=False)\n",
    "    Chem.GetSymmSSSR(cm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "f79a978a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c2ba02344ce74577b38f428c9df1ef35",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(Dropdown(description='idx', options=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 1…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from ipywidgets import interact,fixed\n",
    "from rdkit.Chem.Draw import rdMolDraw2D\n",
    "from IPython.display import SVG\n",
    "@interact(idx=range(0,len(cms)),ms=fixed(cms))\n",
    "def show_mol(idx,ms):\n",
    "    d2d = rdMolDraw2D.MolDraw2DSVG(450,400)\n",
    "    d2d.drawOptions().prepareMolsBeforeDrawing=False\n",
    "    d2d.DrawMolecule(ms[idx])\n",
    "    d2d.FinishDrawing()\n",
    "    return SVG(d2d.GetDrawingText())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3351d6e6",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  "toc": {
   "base_numbering": 1,
   "nav_menu": {},
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   "title_cell": "Table of Contents",
   "title_sidebar": "Contents",
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   "toc_position": {},
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