Morphine

Morphine.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "import py3Dmol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = Chem.AddHs(Chem.MolFromSmiles('CN1CC[C@]23C4=C5C=CC(O)=C4O[C@H]2[C@@H](O)C=C[C@H]3[C@H]1C5'))\n",
    "AllChem.EmbedMolecule(m,useExpTorsionAnglePrefs=True,useBasicKnowledge=True)\n",
    "AllChem.MMFFOptimizeMolecule(m, mmffVariant='MMFF94s')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_14775773971218274\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('http://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "$3Dmolpromise.done(function() {\n",
       "var viewer = $3Dmol.createViewer($(\"#3dmolviewer_14775773971218274\"),{backgroundColor:\"white\"});\n",
       "\tviewer.removeAllModels();\n",
       "\tviewer.addModel(\"\\n     RDKit          3D\\n\\n 40 44  0  0  0  0  0  0  0  0999 V2000\\n   -2.6038    2.9780   -0.7905 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.5014    2.0206   -0.7618 N   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.3345    1.3585   -2.0542 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1779    0.3450   -2.0574 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1339   -0.5220   -0.7741 C   0  0  2  0  0  0  0  0  0  0  0  0\\n    0.9669   -0.0272    0.1172 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.8714    0.9594    1.0848 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.0330    1.2762    1.7942 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.2345    0.5811    1.5444 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.2683   -0.4638    0.6157 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    4.3931   -1.2024    0.4128 O   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.1148   -0.7664   -0.0738 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.9171   -1.8255   -0.9244 O   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.4521   -1.9287   -1.0221 C   0  0  1  0  0  0  0  0  0  0  0  0\\n   -0.0733   -3.0388   -0.0608 C   0  0  1  0  0  0  0  0  0  0  0  0\\n    0.9820   -3.8344    0.4777 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.9293   -2.5829    1.0859 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.5698   -1.4041    1.1167 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.4625   -0.4130   -0.0162 C   0  0  1  0  0  0  0  0  0  0  0  0\\n   -1.5971    1.0946    0.4003 C   0  0  1  0  0  0  0  0  0  0  0  0\\n   -0.4863    1.5252    1.4119 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.6521    3.5399    0.1489 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.4563    3.7145   -1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -3.5691    2.4848   -0.9501 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.1313    2.1048   -2.8325 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2627    0.8520   -2.3506 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.3169   -0.2930   -2.9392 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.7687    0.8799   -2.2122 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.0102    2.0443    2.5638 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    4.1188    0.8453    2.1168 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    5.1037   -0.8448    0.9681 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.2416   -2.2617   -2.0461 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.6956   -3.7233   -0.6506 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.8134   -3.3578    0.2815 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.0573   -3.2852    1.9063 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2154   -1.1656    1.9581 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2978   -0.6620   -0.6865 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.5691    1.2205    0.8972 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.7679    1.1588    2.4077 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.4284    2.6187    1.4811 H   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  2  3  1  0\\n  3  4  1  0\\n  5  4  1  6\\n  5  6  1  0\\n  6  7  2  0\\n  7  8  1  0\\n  8  9  2  0\\n  9 10  1  0\\n 10 11  1  0\\n 10 12  2  0\\n 12 13  1  0\\n 13 14  1  0\\n 14 15  1  0\\n 15 16  1  0\\n 15 17  1  0\\n 17 18  2  0\\n 18 19  1  0\\n 19 20  1  0\\n 20 21  1  0\\n 20  2  1  0\\n 14  5  1  0\\n 19  5  1  0\\n 12  6  1  0\\n 21  7  1  0\\n  1 22  1  0\\n  1 23  1  0\\n  1 24  1  0\\n  3 25  1  0\\n  3 26  1  0\\n  4 27  1  0\\n  4 28  1  0\\n  8 29  1  0\\n  9 30  1  0\\n 11 31  1  0\\n 14 32  1  6\\n 15 33  1  6\\n 16 34  1  0\\n 17 35  1  0\\n 18 36  1  0\\n 19 37  1  6\\n 20 38  1  1\\n 21 39  1  0\\n 21 40  1  0\\nM  END\\n\",\"sdf\");\n",
       "\tviewer.setStyle({\"stick\": {}});\n",
       "\tviewer.zoomTo();\n",
       "viewer.render();\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mb = Chem.MolToMolBlock(m)\n",
    "p = py3Dmol.view(width=400,height=400)\n",
    "p.removeAllModels()\n",
    "p.addModel(mb,'sdf')\n",
    "p.setStyle({'stick':{}})\n",
    "p.zoomTo()\n",
    "p.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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JKkIhHjN58mRyc3P58ssvK9TO559/zujRoyUJCvGMk0QoxGP09fXx9vbm888/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\nAAAASUVORK5CYII=\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x19c96ff14e0>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.5.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}